matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors)

abcrf

Version: 1.9
GitHub: NA
Source code: https://github.com/cran/abcrf
Date/Publication: 2022-08-09 15:30:19 UTC
Number of recursive dependencies: 39

Run revdep_details(, "abcrf") for more info

checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: data 2.6Mb libs 5.3Mb

AlpsNMR

Version: 4.4.0
GitHub: https://github.com/sipss/AlpsNMR
Source code: https://github.com/cran/AlpsNMR
Date/Publication: 2023-10-24
Number of recursive dependencies: 176

Run revdep_details(, "AlpsNMR") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown ! LuaTeX error .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: b ad argument #1 to 'insert' (table expected, got nil) stack traceback: [C]: in function 'insert' .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: in main chunk [C]: in function 'dofile' [string "\directlua "]:6: in main chunk. l.139 } ... LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Vig02-handling-metadata-and-annotations.log for more info. --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’

SUMMARY: processing the following files failed: ‘Vig01-introduction-to-alpsnmr.Rmd’ ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ ‘Vig02-handling-metadata-and-annotations.Rmd’

Error: Vignette re-building failed. Execution halted ```

AMARETTO

Version: 1.18.0
GitHub: NA
Source code: https://github.com/cran/AMARETTO
Date/Publication: 2023-10-24
Number of recursive dependencies: 162

Run revdep_details(, "AMARETTO") for more info

checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'get_firehoseData': get_firehoseData Code: function(TargetDirectory = "./", TCGA_acronym_uppercase = "LUAD", dataType = "stddata", dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType = "tar.gz", gdacURL = "https://gdac.broadinstitute.org/runs/", untarUngzip = TRUE, printDisease_abbr = FALSE) Docs: function(TargetDirectory = "./", TCGA_acronym_uppercase = "LUAD", dataType = "stddata", dataFileTag = "mRNAseq_Preprocess.Level_3", FFPE = FALSE, fileType = "tar.gz", gdacURL = "http://gdac.broadinstitute.org/runs/", untarUngzip = TRUE, printDisease_abbr = FALSE) Mismatches in argument default values: Name: 'gdacURL' Code: "https://gdac.broadinstitute.org/runs/" Docs: "http://gdac.broadinstitute.org/runs/"
checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 1.5Mb doc 2.4Mb
checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: Apache License (== 2.0) + file LICENSE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘knitr’ A package should be listed in only one of these fields. 'LinkingTo' field is unused: package has no 'src' directory
checking R code for possible problems ... NOTE AMARETTO_HTMLreport: no visible binding for global variable ‘ModuleNr’ AMARETTO_HTMLreport: no visible binding for global variable ‘Weights’ AMARETTO_HTMLreport: no visible binding for global variable ‘RegulatorIDs’ AMARETTO_HTMLreport: no visible binding for global variable ‘TargetIDs’ AMARETTO_HTMLreport: no visible binding for global variable ‘moduleNr’ AMARETTO_HTMLreport: no visible binding for global variable ‘Testset’ AMARETTO_HTMLreport: no visible binding for global variable ‘padj’ AMARETTO_HTMLreport: no visible binding for global variable ‘n_Overlapping’ ... GmtFromModules: no visible binding for global variable ‘GeneNames’ HyperGTestGeneEnrichment: no visible binding for global variable ‘i’ HyperGTestGeneEnrichment: no visible binding for global variable ‘j’ read_gct: no visible binding for global variable ‘Description’ Undefined global functions or variables: Color Description GeneNames Genes Geneset Geneset_length ModuleNr Modules MsigdbMapping NumberGenes Overlapping_genes RegulatorIDs TargetIDs Testset Type Weights dt_gensesetsall i j moduleNr n_Overlapping overlap_perc p.value p_value padj q.value value variable
checking data for non-ASCII characters ... NOTE Note: found 152 marked UTF-8 strings

amplican

Version: 1.24.0
GitHub: https://github.com/valenlab/amplican
Source code: https://github.com/cran/amplican
Date/Publication: 2023-10-24
Number of recursive dependencies: 131

Run revdep_details(, "amplican") for more info

checking installed package size ... NOTE installed size is 16.2Mb sub-directories of 1Mb or more: doc 13.7Mb libs 1.6Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘CrispRVariants’

aroma.core

Version: 3.3.0
GitHub: https://github.com/HenrikBengtsson/aroma.core
Source code: https://github.com/cran/aroma.core
Date/Publication: 2022-11-15 18:30:13 UTC
Number of recursive dependencies: 72

Run revdep_details(, "aroma.core") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

aroma.light

Version: 3.32.0
GitHub: https://github.com/HenrikBengtsson/aroma.light
Source code: https://github.com/cran/aroma.light
Date/Publication: 2023-10-24
Number of recursive dependencies: 6

Run revdep_details(, "aroma.light") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/rsp/.rspPlugins These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

autonomics

Version: 1.9.0
GitHub: https://github.com/bhagwataditya/autonomics
Source code: https://github.com/cran/autonomics
Date/Publication: 2023-05-21
Number of recursive dependencies: 218

Run revdep_details(, "autonomics") for more info

checking examples ... ERROR ``` Running examples in ‘autonomics-Ex.R’ failed The error most likely occurred in:

Name: center

Title: Center samples

Aliases: center

** Examples

require(magrittr) ... Retain 6692/6735 features: contaminant != '+' Retain 6679/6692 features: non-zero, non-NA, and non-NaN for some sample Filter 4534/6679 features: expr > 0 for at least two samples in some subgroup Transform exprs fdata(object)$housekeeping <- FALSE fdata(object)$housekeeping[order(rowVars(values(object)))[1:100]] <- TRUE Error in rowVars(values(object)) : Argument 'x' must be a matrix or a vector. Calls: order -> standardGeneric -> eval -> eval -> eval -> rowVars Execution halted ```
checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'normimpute' ‘ref’ ‘pos’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

bahc

Version: 0.3.0
GitHub: NA
Source code: https://github.com/cran/bahc
Date/Publication: 2020-09-21 16:40:02 UTC
Number of recursive dependencies: 2

Run revdep_details(, "bahc") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

BASiCS

Version: 2.14.0
GitHub: https://github.com/catavallejos/BASiCS
Source code: https://github.com/cran/BASiCS
Date/Publication: 2023-10-24
Number of recursive dependencies: 195

Run revdep_details(, "BASiCS") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 14.4Mb sub-directories of 1Mb or more: data 2.0Mb doc 1.4Mb libs 10.1Mb

BatchQC

Version: 1.30.0
GitHub: https://github.com/mani2012/BatchQC
Source code: https://github.com/cran/BatchQC
Date/Publication: 2023-10-24
Number of recursive dependencies: 164

Run revdep_details(, "BatchQC") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: ... --- re-building ‘BatchQCIntro.Rmd’ using rmarkdown --- finished re-building ‘BatchQCIntro.Rmd’

--- re-building ‘BatchQC_examples.Rmd’ using rmarkdown --- finished re-building ‘BatchQC_examples.Rmd’

--- re-building ‘BatchQC_usage_advanced.Rmd’ using rmarkdown ! LaTeX Error: File `iftex.sty' not found. ...

Error: processing vignette 'BatchQC_usage_advanced.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/BatchQC/new/BatchQC.Rcheck/vign_test/BatchQC/vignettes/BatchQC_usage_advanced.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See BatchQC_usage_advanced.log for more info. --- failed re-building ‘BatchQC_usage_advanced.Rmd’

SUMMARY: processing the following file failed: ‘BatchQC_usage_advanced.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking R code for possible problems ... NOTE gene_plot: no visible global function definition for ‘boxplot’ gene_plot: no visible binding for global variable ‘batch’ gls.series.C: no visible global function definition for ‘lm.fit’ sample_plot: no visible global function definition for ‘boxplot’ sample_plot: no visible binding for global variable ‘batch’ Undefined global functions or variables: batch boxplot lm.fit Consider adding importFrom("graphics", "boxplot") importFrom("stats", "lm.fit") to your NAMESPACE file.

BayesfMRI

Version: 0.3.5
GitHub: https://github.com/mandymejia/BayesfMRI
Source code: https://github.com/cran/BayesfMRI
Date/Publication: 2023-06-08 17:52:54 UTC
Number of recursive dependencies: 125

Run revdep_details(, "BayesfMRI") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’
checking installed package size ... NOTE installed size is 16.1Mb sub-directories of 1Mb or more: libs 15.8Mb

BayesianPlatformDesignTimeTrend

Version: 1.2.1
GitHub: https://github.com/ZXW834/BayesianPlatformDesignTimeTrend
Source code: https://github.com/cran/BayesianPlatformDesignTimeTrend
Date/Publication: 2023-10-11 13:30:05 UTC
Number of recursive dependencies: 123

Run revdep_details(, "BayesianPlatformDesignTimeTrend") for more info

checking installed package size ... NOTE installed size is 109.8Mb sub-directories of 1Mb or more: data 1.3Mb help 1.8Mb libs 105.6Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

baystability

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/baystability
Date/Publication: 2018-03-13 15:55:34 UTC
Number of recursive dependencies: 128

Run revdep_details(, "baystability") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’ All declared Imports should be used.

bigPint

Version: 1.15.0
GitHub: https://github.com/lindsayrutter/bigPint
Source code: https://github.com/cran/bigPint
Date/Publication: 2022-11-01
Number of recursive dependencies: 177

Run revdep_details(, "bigPint") for more info

checking examples ... ERROR ``` Running examples in ‘bigPint-Ex.R’ failed The error most likely occurred in:

Name: plotClusters

Title: Plot static parallel coordinate clusters

Aliases: plotClusters

** Examples

The first set of five examples use data and dataMetrics

... data(soybean_ir_sub) soybean_ir_sub[,-1] <- log(soybean_ir_sub[-1]+1) data(soybean_ir_sub_metrics) colList = c("#00A600FF", rainbow(5)[c(1,4,5)]) ret <- plotClusters(data=soybean_ir_sub, + dataMetrics = soybean_ir_sub_metrics, nC=4, colList = colList, + clusterAllData = FALSE, threshVal = 1e-7, saveFile = FALSE) Error in xtfrm.data.frame(x) : cannot xtfrm data frames Calls: plotClusters ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame Execution halted ```
checking tests ... ``` Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Complete output: > BiocGenerics:::testPackage("bigPint") Error in xtfrm.data.frame(x) : cannot xtfrm data frames Error in xtfrm.data.frame(x) : cannot xtfrm data frames Error in xtfrm.data.frame(x) : cannot xtfrm data frames Error in xtfrm.data.frame(x) : cannot xtfrm data frames

... test_dataMetricsVolcano.R /c4/home/henrik/repositories/matrixStats/revdep/checks/bigPint/new/bigPint.Rcheck/bigPint/unitTests/test_dataMetricsVolcano.R
```
 test_dataMetricsVolcanoApp.R 
   /c4/home/henrik/repositories/matrixStats/revdep/checks/bigPint/new/bigPint.Rcheck/bigPint/unitTests/test_dataMetricsVolcanoApp.R
```
Error in BiocGenerics:::testPackage("bigPint") : unit tests failed for package bigPint Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘bioconductor.Rmd’ using rmarkdown Error: processing vignette 'bioconductor.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘bioconductor.Rmd’

--- re-building ‘manuscripts.Rmd’ using rmarkdown Error: processing vignette 'manuscripts.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ ... --- re-building ‘summarizedExperiment.Rmd’ using rmarkdown Error: processing vignette 'summarizedExperiment.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘summarizedExperiment.Rmd’

SUMMARY: processing the following files failed: ‘bioconductor.Rmd’ ‘manuscripts.Rmd’ ‘summarizedExperiment.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: data 2.0Mb doc 2.3Mb shiny-examples 3.0Mb

bingat

Version: 1.3
GitHub: NA
Source code: https://github.com/cran/bingat
Date/Publication: 2017-07-05 18:30:37 UTC
Number of recursive dependencies: 32

Run revdep_details(, "bingat") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘genalg’

BioNERO

Version: 1.10.0
GitHub: https://github.com/almeidasilvaf/BioNERO
Source code: https://github.com/cran/BioNERO
Date/Publication: 2023-10-24
Number of recursive dependencies: 179

Run revdep_details(, "BioNERO") for more info

checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: data 2.2Mb doc 4.3Mb

biscuiteer

Version: 1.16.0
GitHub: https://github.com/trichelab/biscuiteer
Source code: https://github.com/cran/biscuiteer
Date/Publication: 2023-10-24
Number of recursive dependencies: 223

Run revdep_details(, "biscuiteer") for more info

checking whether package ‘biscuiteer’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/biscuiteer/new/biscuiteer.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: data 1.1Mb extdata 3.4Mb
checking package subdirectories ... NOTE Problems with news in ‘NEWS.md’: No news entries found.
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘QDNAseq:::expectedVariance’ See the note in ?`:::` about the use of this operator.

blackbox

Version: 1.1.43
GitHub: NA
Source code: https://github.com/cran/blackbox
Date/Publication: 2023-05-03 07:30:06 UTC
Number of recursive dependencies: 67

Run revdep_details(, "blackbox") for more info

checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: libs 8.9Mb

BloodGen3Module

Version: 1.10.0
GitHub: NA
Source code: https://github.com/cran/BloodGen3Module
Date/Publication: 2023-10-24
Number of recursive dependencies: 176

Run revdep_details(, "BloodGen3Module") for more info

checking whether package ‘BloodGen3Module’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘SummarizedExperiment::rowRanges’ by ‘matrixStats::rowRanges’ when loading ‘BloodGen3Module’ Warning: replacing previous import ‘SummarizedExperiment::start’ by ‘stats::start’ when loading ‘BloodGen3Module’ Warning: replacing previous import ‘SummarizedExperiment::end’ by ‘stats::end’ when loading ‘BloodGen3Module’ Warning: replacing previous import ‘matrixStats::rowRanges’ by ‘SummarizedExperiment::rowRanges’ when loading ‘BloodGen3Module’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/BloodGen3Module/new/BloodGen3Module.Rcheck/00install.out’ for details.
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.

bnbc

Version: 1.23.0
GitHub: https://github.com/hansenlab/bnbc
Source code: https://github.com/cran/bnbc
Date/Publication: 2023-05-21
Number of recursive dependencies: 104

Run revdep_details(, "bnbc") for more info

checking Rd files ... WARNING checkRd: (5) ContactGroup-class.Rd:72-74: \item in \describe must have non-empty label
checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: data 2.4Mb libs 1.7Mb

bnclassify

Version: 0.4.7
GitHub: https://github.com/bmihaljevic/bnclassify
Source code: https://github.com/cran/bnclassify
Date/Publication: 2022-11-16 12:11:13 UTC
Number of recursive dependencies: 107

Run revdep_details(, "bnclassify") for more info

checking tests ... `` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(bnclassify) > > test_check("bnclassify") -1.54485 -1.50696 -1.31785 -1.2128 -1.4612 -1.20742 -1.26966 -1.67055 -0.440312 -1.11241 -4.29046 -4.29046 -0.545227 -0.93827 -4.23411 -4.23411 [ FAIL 2 | WARN 0 | SKIP 39 | PASS 587 ] ... ── Error ('test-dag.R:8:3'): Condition on ────────────────────────────────────── Error ingraphNEL2_graph_internal(g)`: inherits(x, "graphNEL") is not TRUE Backtrace: ▆
1. └─bnclassify:::graphNEL2_graph_internal(g) at test-dag.R:8:2
2. └─base::stopifnot(inherits(x, "graphNEL"))
[ FAIL 2 | WARN 0 | SKIP 39 | PASS 587 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: --- re-building ‘methods.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'methods.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/bnclassify/new/bnclassify.Rcheck/vign_test/bnclassify/vignettes/methods.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See methods.log for more info. --- failed re-building ‘methods.Rmd’ ...

Error: processing vignette 'usage.rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/bnclassify/new/bnclassify.Rcheck/vign_test/bnclassify/vignettes/usage.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See usage.log for more info. --- failed re-building ‘usage.rmd’

SUMMARY: processing the following files failed: ‘methods.Rmd’ ‘overview.Rmd’ ‘usage.rmd’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 11.0Mb sub-directories of 1Mb or more: libs 10.3Mb

bnem

Version: 1.10.0
GitHub: https://github.com/MartinFXP/bnem
Source code: https://github.com/cran/bnem
Date/Publication: 2023-10-24
Number of recursive dependencies: 169

Run revdep_details(, "bnem") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rmarkdown’ All declared Imports should be used.

brms

Version: 2.20.4
GitHub: https://github.com/paul-buerkner/brms
Source code: https://github.com/cran/brms
Date/Publication: 2023-09-25 19:00:09 UTC
Number of recursive dependencies: 200

Run revdep_details(, "brms") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: R 3.0Mb doc 3.5Mb

BSgenome

Version: 1.70.0
GitHub: https://github.com/Bioconductor/BSgenome
Source code: https://github.com/cran/BSgenome
Date/Publication: 2023-10-24
Number of recursive dependencies: 105

Run revdep_details(, "BSgenome") for more info

checking examples ... ERROR ``` Running examples in ‘BSgenome-Ex.R’ failed The error most likely occurred in:

Name: SNPlocs-class

Title: SNPlocs objects

Aliases: class:SNPlocs SNPlocs-class SNPlocs class:ODLT_SNPlocs

ODLT_SNPlocs-class ODLT_SNPlocs class:OldFashionSNPlocs

OldFashionSNPlocs-class OldFashionSNPlocs provider,SNPlocs-method

providerVersion,SNPlocs-method releaseDate,SNPlocs-method releaseName

releaseName,SNPlocs-method referenceGenome

... seqlevelsStyle(my_cds) # UCSC [1] "UCSC" seqlevelsStyle(snps) # NCBI [1] "NCBI" seqlevelsStyle(my_cds) <- seqlevelsStyle(snps) Error in find_NCBI_assembly_ftp_dir(assembly_accession, assembly_name = assembly_name) : unable to find FTP dir for assembly GCF_000001405.40 in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/ Calls: seqlevelsStyle<- ... .form_assembly_report_url -> find_NCBI_assembly_ftp_dir Execution halted ```
checking for missing documentation entries ... WARNING Undocumented code objects: ‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘OnDiskLongTable_old’ ‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’ ‘forgeMaskedBSgenomeDataPkg’ ‘getBatchesByOverlapsFromOnDiskLongTable’ ‘getBatchesBySeqnameFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’ ‘getRowsByIdFromOnDiskLongTable’ ‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’ ‘saveAsOnDiskLongTable_old’ ‘saveRowidsForOnDiskLongTable_old’ ... generic 'seqinfo' and siglist 'TwobitNamedSequences' generic 'seqnames' and siglist 'OnDiskNamedSequences' generic 'show' and siglist 'OnDiskLongTable' generic 'show' and siglist 'OnDiskLongTable_old' generic 'show' and siglist 'OnDiskNamedSequences' generic 'spatialIndex' and siglist 'OnDiskLongTable' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'Biostrings', 'BiocIO', 'rtracklayer' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for portable file names ... NOTE ``` Found the following non-portable file path: BSgenome/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R

Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ```
checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: R 1.7Mb extdata 5.5Mb
checking package subdirectories ... NOTE Found the following CITATION file in a non-standard place: inst/extdata/GentlemanLab/BSgenome.Creinhardtii.JGI.v5.6-tools/CITATION Most likely ‘inst/CITATION’ should be used instead.
checking dependencies in R code ... NOTE ':::' calls which should be '::': ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’ ‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’ See the note in ?`:::` about the use of this operator.

BSW

Version: 0.1.1
GitHub: https://github.com/adam-bec/BSW
Source code: https://github.com/cran/BSW
Date/Publication: 2021-03-22 16:20:09 UTC
Number of recursive dependencies: 56

Run revdep_details(, "BSW") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

bulkAnalyseR

Version: 1.1.0
GitHub: https://github.com/Core-Bioinformatics/bulkAnalyseR
Source code: https://github.com/cran/bulkAnalyseR
Date/Publication: 2022-12-15 12:20:02 UTC
Number of recursive dependencies: 201

Run revdep_details(, "bulkAnalyseR") for more info

checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 2.3Mb extdata 3.4Mb

bumphunter

Version: 1.44.0
GitHub: https://github.com/rafalab/bumphunter
Source code: https://github.com/cran/bumphunter
Date/Publication: 2023-10-24
Number of recursive dependencies: 117

Run revdep_details(, "bumphunter") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'foreach', 'iterators', 'parallel', 'locfit' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘doParallel:::.options’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE bumphunterEngine: no visible binding for global variable ‘bootstraps’ Undefined global functions or variables: bootstraps

CARBayesST

Version: 4.0
GitHub: https://github.com/duncanplee/CARBayesST
Source code: https://github.com/cran/CARBayesST
Date/Publication: 2023-10-30 16:40:02 UTC
Number of recursive dependencies: 107

Run revdep_details(, "CARBayesST") for more info

checking installed package size ... NOTE installed size is 11.3Mb sub-directories of 1Mb or more: R 1.0Mb libs 9.2Mb

cardelino

Version: 1.4.0
GitHub: https://github.com/single-cell-genetics/cardelino
Source code: https://github.com/cran/cardelino
Date/Publication: 2023-10-24
Number of recursive dependencies: 161

Run revdep_details(, "cardelino") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doMC’

CATALYST

Version: 1.26.0
GitHub: https://github.com/HelenaLC/CATALYST
Source code: https://github.com/cran/CATALYST
Date/Publication: 2023-10-24
Number of recursive dependencies: 218

Run revdep_details(, "CATALYST") for more info

checking installed package size ... NOTE installed size is 14.4Mb sub-directories of 1Mb or more: data 3.1Mb doc 10.0Mb
checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.cluster_cols’

causalOT

Version: 0.1.2
GitHub: NA
Source code: https://github.com/cran/causalOT
Date/Publication: 2022-09-04 14:30:12 UTC
Number of recursive dependencies: 115

Run revdep_details(, "causalOT") for more info

checking C++ specification ... NOTE Specified C++14: please drop specification unless essential
checking installed package size ... NOTE installed size is 36.0Mb sub-directories of 1Mb or more: R 1.6Mb libs 34.2Mb

ccImpute

Version: 1.4.0
GitHub: https://github.com/khazum/ccImpute
Source code: https://github.com/cran/ccImpute
Date/Publication: 2023-10-24
Number of recursive dependencies: 191

Run revdep_details(, "ccImpute") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: libs 7.4Mb

celda

Version: 1.17.0
GitHub: https://github.com/campbio/celda
Source code: https://github.com/cran/celda
Date/Publication: 2023-05-23
Number of recursive dependencies: 381

Run revdep_details(, "celda") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘singleCellTK’
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 11.8Mb sub-directories of 1Mb or more: doc 3.2Mb libs 7.2Mb

CelliD

Version: 1.10.0
GitHub: NA
Source code: https://github.com/cran/CelliD
Date/Publication: 2023-10-24
Number of recursive dependencies: 278

Run revdep_details(, "CelliD") for more info

checking examples ... ERROR ``` Running examples in ‘CelliD-Ex.R’ failed The error most likely occurred in:

Name: DimPlotMC

Title: Seurat DimPlot for MCA like Dimensionality Reduction

Aliases: DimPlotMC

** Examples

seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5) Error in (function (cond) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': assay must be one of "RNA", not "data". Calls: RunMCA ... abort -> signal_abort -> signalCondition -> Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 2. ├─CelliD:::RunMCA.Seurat(seurat, nmcs = 10) 3. │ ├─base::as.matrix(GetAssayData(X, slot)) 4. │ ├─SeuratObject::GetAssayData(X, slot) 5. │ └─SeuratObject:::GetAssayData.Seurat(X, slot) 6. │ └─rlang::arg_match(arg = assay, values = Assays(object = object)) 7. │ └─rlang::arg_match0(arg, values, error_arg, error_call = error_call) ... 7. │ └─rlang::arg_match0(arg, values, error_arg, error_call = error_call) 8. ├─rlang:::stop_arg_match(w, values = x, error_arg = y, error_call = z) 9. │ └─rlang::abort(msg, call = error_call, arg = error_arg)
1. │ └─rlang:::signal_abort(cnd, .file)
2. │ └─base::signalCondition(cnd)
3. └─base (local) <fn>(<rlng_rrr>)
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 9 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘BioconductorVignette.Rmd’ using rmarkdown Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ********|

| | | 0% | ... Quitting from lines 98-99 [MCA1] (BioconductorVignette.Rmd) Error: processing vignette 'BioconductorVignette.Rmd' failed with diagnostics: error in evaluating the argument 'x' in selecting a method for function 'as.matrix': assay must be one of "RNA", not "data". --- failed re-building ‘BioconductorVignette.Rmd’

SUMMARY: processing the following file failed: ‘BioconductorVignette.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking whether package ‘CelliD’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘data.table::shift’ by ‘tictoc::shift’ when loading ‘CelliD’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/CelliD/new/CelliD.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: doc 3.1Mb libs 3.4Mb

cellWise

Version: 2.5.3
GitHub: NA
Source code: https://github.com/cran/cellWise
Date/Publication: 2023-10-25 13:00:02 UTC
Number of recursive dependencies: 70

Run revdep_details(, "cellWise") for more info

checking installed package size ... NOTE installed size is 19.8Mb sub-directories of 1Mb or more: data 3.1Mb doc 1.9Mb libs 14.3Mb

CEMiTool

Version: 1.26.0
GitHub: NA
Source code: https://github.com/cran/CEMiTool
Date/Publication: 2023-10-24
Number of recursive dependencies: 215

Run revdep_details(, "CEMiTool") for more info

checking installed package size ... NOTE installed size is 8.8Mb sub-directories of 1Mb or more: data 3.1Mb doc 2.3Mb extdata 2.8Mb
checking R code for possible problems ... NOTE flip_vector: no visible global function definition for ‘setNames’ select_genes: no visible global function definition for ‘var’ get_hubs,CEMiTool : <anonymous>: no visible global function definition for ‘head’ get_merged_mods,CEMiTool: no visible global function definition for ‘as.dist’ get_mods,CEMiTool: no visible global function definition for ‘as.dist’ get_phi,CEMiTool: no visible global function definition for ‘tail’ get_phi,CEMiTool: no visible global function definition for ‘head’ mod_gene_num,CEMiTool: no visible binding for global variable ‘modules’ ... save_plots,CEMiTool: no visible global function definition for ‘dev.off’ Undefined global functions or variables: ..eq.label.. ..rr.label.. := Mean Variance as.dist data dev.off dist head modules num_genes setNames tail var Consider adding importFrom("grDevices", "dev.off") importFrom("stats", "as.dist", "dist", "setNames", "var") importFrom("utils", "data", "head", "tail") to your NAMESPACE file.

ChAMP

Version: 2.30.0
GitHub: NA
Source code: https://github.com/cran/ChAMP
Date/Publication: 2023-04-25
Number of recursive dependencies: 247

Run revdep_details(, "ChAMP") for more info

checking whether package ‘ChAMP’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores) Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ChAMP/new/ChAMP.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’.
checking Rd \usage sections ... WARNING ``` Duplicated \argument entries in documentation object 'champ.SVD': ‘Rplot’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'minfi', 'ChAMPdata', 'DMRcate', 'Illumina450ProbeVariants.db', 'IlluminaHumanMethylationEPICmanifest', 'DT', 'RPMM' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: doc 3.6Mb extdata 1.9Mb
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘rmarkdown’ A package should be listed in only one of these fields.
checking startup messages can be suppressed ... NOTE ``` No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'prettydoc' All declared Imports should be used. Package in Depends field not imported from: 'DT' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE champ.DMR: possible error in dmrcate(myannotation, min.cpgs = minProbes, lambda = lambda, C = C, mc.cores = cores): unused argument (mc.cores = cores) champ.ebGSEA : gseaWTfn: no visible global function definition for 'wilcox.test' champ.ebGSEA: no visible global function definition for 'stopCluster' champ.norm: no visible global function definition for 'stopCluster' champ.process: no visible global function definition for 'champ.EpiMod' Undefined global functions or variables: champ.EpiMod stopCluster wilcox.test Consider adding importFrom("stats", "wilcox.test") to your NAMESPACE file.

ChemoSpec2D

Version: 0.5.0
GitHub: https://github.com/bryanhanson/ChemoSpec2D
Source code: https://github.com/cran/ChemoSpec2D
Date/Publication: 2021-10-11 07:40:38 UTC
Number of recursive dependencies: 101

Run revdep_details(, "ChemoSpec2D") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘ChemoSpec2D.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'ChemoSpec2D.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/ChemoSpec2D/new/ChemoSpec2D.Rcheck/vign_test/ChemoSpec2D/vignettes/ChemoSpec2D.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See ChemoSpec2D.log for more info. --- failed re-building ‘ChemoSpec2D.Rmd’

SUMMARY: processing the following file failed: ‘ChemoSpec2D.Rmd’

Error: Vignette re-building failed. Execution halted ```

ChIPpeakAnno

Version: 3.36.0
GitHub: NA
Source code: https://github.com/cran/ChIPpeakAnno
Date/Publication: 2023-10-24
Number of recursive dependencies: 235

Run revdep_details(, "ChIPpeakAnno") for more info

checking examples ... ERROR ``` Running examples in ‘ChIPpeakAnno-Ex.R’ failed The error most likely occurred in:

Name: findEnhancers

Title: Find possible enhancers depend on DNA interaction data

Aliases: findEnhancers

Keywords: misc

** Examples

...

Try to keep the seqname style consistent.

Try to keep the seqname style consistent.

data("myPeakList") findEnhancers(myPeakList[500:1000], annoData, DNAinteractiveData) Error in findEnhancers(myPeakList[500:1000], annoData, DNAinteractiveData) : length(intersect(seqlevelsStyle(peaks), seqlevelsStyle(annoData))) > .... is not TRUE Calls: findEnhancers -> stopifnot Execution halted ```
checking tests ... ``` Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 50 lines of output: INFO [2023-11-01 23:52:30] INFO [2023-11-01 23:52:30] $x INFO [2023-11-01 23:52:30] $x$TF1 INFO [2023-11-01 23:52:30] [1] 3 4 5 INFO [2023-11-01 23:52:30] INFO [2023-11-01 23:52:30] $x$TF2 ... 6. └─BSgenome (local) .local(x, ...) 7. └─BSgenome:::.extractFromBSgenomeMultipleSequences(...) 8. ├─BiocGenerics::lapply(...) 9. └─base::lapply(...)
1. └─BSgenome (local) FUN(X[[i]], ...)
2. └─BSgenome:::.getOneSeqFromBSgenomeMultipleSequences(...)
[ FAIL 1 | WARN 2 | SKIP 6 | PASS 312 ] Error: Test failures Execution halted ```
checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘ChIPpeakAnno.Rmd’ using rmarkdown --- finished re-building ‘ChIPpeakAnno.Rmd’

--- re-building ‘FAQs.Rmd’ using rmarkdown --- finished re-building ‘FAQs.Rmd’

--- re-building ‘pipeline.Rmd’ using rmarkdown

Quitting from lines 154-166 [workflow3] (pipeline.Rmd) ... Quitting from lines 65-72 [annotate] (quickStart.Rmd) Error: processing vignette 'quickStart.Rmd' failed with diagnostics: 'length.out' must be a non-negative number --- failed re-building ‘quickStart.Rmd’

SUMMARY: processing the following files failed: ‘pipeline.Rmd’ ‘quickStart.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 25.2Mb sub-directories of 1Mb or more: data 12.6Mb doc 6.2Mb extdata 5.2Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ensembldb’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) assignChromosomeRegion.Rd:133: Escaped LaTeX specials: \_

chromswitch

Version: 1.22.0
GitHub: https://github.com/sjessa/chromswitch
Source code: https://github.com/cran/chromswitch
Date/Publication: 2023-04-25
Number of recursive dependencies: 186

Run revdep_details(, "chromswitch") for more info

checking whether package ‘chromswitch’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'chromswitch' is deprecated and will be removed from See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/chromswitch/new/chromswitch.Rcheck/00install.out’ for details.

cifti

Version: 0.4.5
GitHub: NA
Source code: https://github.com/cran/cifti
Date/Publication: 2018-02-01 23:25:24 UTC
Number of recursive dependencies: 54

Run revdep_details(, "cifti") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

cliqueMS

Version: 1.16.0
GitHub: https://github.com/osenan/cliqueMS
Source code: https://github.com/cran/cliqueMS
Date/Publication: 2023-10-24
Number of recursive dependencies: 173

Run revdep_details(, "cliqueMS") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 9.2Mb sub-directories of 1Mb or more: libs 7.6Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘MSnbase’ All declared Imports should be used.

clusterExperiment

Version: 2.22.0
GitHub: https://github.com/epurdom/clusterExperiment
Source code: https://github.com/cran/clusterExperiment
Date/Publication: 2023-10-24
Number of recursive dependencies: 184

Run revdep_details(, "clusterExperiment") for more info

checking contents of ‘data’ directory ... WARNING Output for data("rsecFluidigm", package = "clusterExperiment"): Search path was changed
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 18.0Mb sub-directories of 1Mb or more: R 1.3Mb data 3.6Mb doc 10.4Mb libs 2.2Mb
checking foreign function calls ... NOTE Foreign function calls to a different package: .C(ape::node_depth, ...) .C(ape::node_depth_edgelength, ...) .C(ape::node_height, ...) .C(ape::node_height_clado, ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘scRNAseq’, ‘ConsensusClusterPlus’

clustifyr

Version: 1.14.0
GitHub: https://github.com/rnabioco/clustifyr
Source code: https://github.com/cran/clustifyr
Date/Publication: 2023-10-24
Number of recursive dependencies: 202

Run revdep_details(, "clustifyr") for more info

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: data 2.1Mb doc 1.5Mb help 1.1Mb
checking R code for possible problems ... NOTE gmt_to_list: no visible global function definition for ‘read.csv’ Undefined global functions or variables: read.csv Consider adding importFrom("utils", "read.csv") to your NAMESPACE file.

cmapR

Version: 1.14.0
GitHub: https://github.com/cmap/cmapR
Source code: https://github.com/cran/cmapR
Date/Publication: 2023-10-24
Number of recursive dependencies: 85

Run revdep_details(, "cmapR") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .dockerignore docs/build/html/.buildinfo These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 2.3Mb extdata 2.1Mb
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocManager’ 'library' or 'require' call not declared from: ‘BiocManager’

cna

Version: 3.5.4
GitHub: NA
Source code: https://github.com/cran/cna
Date/Publication: 2023-08-10 18:00:11 UTC
Number of recursive dependencies: 72

Run revdep_details(, "cna") for more info

checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: libs 7.8Mb
checking re-building of vignette outputs ... NOTE `` Error(s) in re-building vignettes: --- re-building ‘cna.Rnw’ using Sweave Registered S3 method overwritten by 'cna': method from some.data.frame car Error: processing vignette 'cna.Rnw' failed with diagnostics: Running 'texi2dvi' on 'cna.tex' failed. LaTeX errors: ! LaTeX Error: Filenicefrac.sty' not found.

... l.12 \usepackage {float}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building 'cna.Rnw'

SUMMARY: processing the following file failed: 'cna.Rnw'

Error: Vignette re-building failed. Execution halted ```

CNVScope

Version: 3.7.2
GitHub: https://github.com/jamesdalg/CNVScope
Source code: https://github.com/cran/CNVScope
Date/Publication: 2022-03-30 23:40:08 UTC
Number of recursive dependencies: 205

Run revdep_details(, "CNVScope") for more info

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: doc 3.2Mb extdata 1.7Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'Hmisc' All declared Imports should be used.

coin

Version: 1.4-3
GitHub: NA
Source code: https://github.com/cran/coin
Date/Publication: 2023-09-27 16:10:02 UTC
Number of recursive dependencies: 20

Run revdep_details(, "coin") for more info

checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘Implementation.Rnw’ using Sweave Loading required package: survival Loading required package: grid --- finished re-building ‘Implementation.Rnw’

--- re-building ‘LegoCondInf.Rnw’ using Sweave Loading required package: coin Loading required package: survival Error: processing vignette 'LegoCondInf.Rnw' failed with diagnostics: ... Warning in .local(object, ...) : p-values may be incorrect due to violation of the subset pivotality condition --- finished re-building ‘coin.Rnw’

SUMMARY: processing the following file failed: ‘LegoCondInf.Rnw’

Error: Vignette re-building failed. Execution halted ```

cola

Version: 2.8.0
GitHub: https://github.com/jokergoo/cola
Source code: https://github.com/cran/cola
Date/Publication: 2023-10-24
Number of recursive dependencies: 254

Run revdep_details(, "cola") for more info

checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: data 3.2Mb extdata 1.0Mb libs 2.3Mb

compcodeR

Version: 1.38.0
GitHub: https://github.com/csoneson/compcodeR
Source code: https://github.com/cran/compcodeR
Date/Publication: 2023-10-24
Number of recursive dependencies: 207

Run revdep_details(, "compcodeR") for more info

checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'rpanel', 'DSS'

condiments

Version: 1.10.0
GitHub: https://github.com/HectorRDB/condiments
Source code: https://github.com/cran/condiments
Date/Publication: 2023-10-24
Number of recursive dependencies: 226

Run revdep_details(, "condiments") for more info

checking R code for possible problems ... NOTE .condition_sling: no visible binding for global variable ‘.’ .condition_sling : <anonymous>: no visible binding for global variable ‘.’ .distinct_inputs: no visible binding for global variable ‘Samples’ .distinct_inputs: no visible binding for global variable ‘.’ .fateSelectionTest: no visible binding for global variable ‘pair’ .fateSelectionTest: no visible binding for global variable ‘statistic’ .fateSelectionTest: no visible binding for global variable ‘p.value’ .multiple_samples: no visible binding for global variable ‘p.value’ .progressionTest: no visible binding for global variable ‘lineage’ ... .progressionTest: no visible binding for global variable ‘statistic’ .progressionTest: no visible binding for global variable ‘p.value’ .topologyTest_multipleSamples: no visible binding for global variable ‘p.value’ fateSelectionTest_multipleSamples,SlingshotDataSet: no visible binding for global variable ‘condition’ progressionTest_multipleSamples,SlingshotDataSet: no visible binding for global variable ‘condition’ Undefined global functions or variables: . Samples condition lineage p.value pair statistic

conquer

Version: 1.3.3
GitHub: https://github.com/XiaoouPan/conquer
Source code: https://github.com/cran/conquer
Date/Publication: 2023-03-06 08:40:02 UTC
Number of recursive dependencies: 5

Run revdep_details(, "conquer") for more info

checking installed package size ... NOTE installed size is 23.3Mb sub-directories of 1Mb or more: libs 23.1Mb

cophescan

Version: 1.3.2
GitHub: https://github.com/ichcha-m/cophescan
Source code: https://github.com/cran/cophescan
Date/Publication: 2023-10-25 07:00:06 UTC
Number of recursive dependencies: 111

Run revdep_details(, "cophescan") for more info

checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: data 3.5Mb libs 3.1Mb

corrcoverage

Version: 1.2.1
GitHub: https://github.com/annahutch/corrcoverage
Source code: https://github.com/cran/corrcoverage
Date/Publication: 2019-12-06 23:20:12 UTC
Number of recursive dependencies: 77

Run revdep_details(, "corrcoverage") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: extdata 3.8Mb libs 1.4Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘data.table’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

crlmm

Version: 1.60.0
GitHub: NA
Source code: https://github.com/cran/crlmm
Date/Publication: 2023-10-24
Number of recursive dependencies: 64

Run revdep_details(, "crlmm") for more info

checking Rd files ... WARNING checkRd: (5) CNSet-methods.Rd:39-41: \item in \describe must have non-empty label checkRd: (5) CNSet-methods.Rd:65-67: \item in \describe must have non-empty label checkRd: (5) CNSet-methods.Rd:69-71: \item in \describe must have non-empty label checkRd: (-1) constructInf.Rd:35: Escaped LaTeX specials: \_ \_ checkRd: (-1) genotype.Illumina.Rd:48: Escaped LaTeX specials: \_ \_ checkRd: (-1) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:39: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:56: Escaped LaTeX specials: \_ checkRd: (-1) snprma.Rd:38: Escaped LaTeX specials: \_ \_
checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: R 1.2Mb data 2.7Mb
checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for ‘preprocessCore’ is only usable in R >= 3.0.2
checking startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘RUnit’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘splines’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .test: no visible global function definition for ‘defineTestSuite’ .test: no visible global function definition for ‘runTestSuite’ .test: no visible global function definition for ‘printTextProtocol’ calculateRBafCNSet : processByChromosome: no visible global function definition for ‘position’ genotypeInf: no visible binding for global variable ‘anno’ krlmm: no visible binding for global variable ‘VGLMparameters’ Undefined global functions or variables: VGLMparameters anno defineTestSuite position printTextProtocol runTestSuite

crossmeta

Version: 1.28.0
GitHub: https://github.com/alexvpickering/crossmeta
Source code: https://github.com/cran/crossmeta
Date/Publication: 2023-10-24
Number of recursive dependencies: 162

Run revdep_details(, "crossmeta") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RCurl’ ‘XML’ All declared Imports should be used.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘GeneMeta’

cSEM

Version: 0.5.0
GitHub: https://github.com/M-E-Rademaker/cSEM
Source code: https://github.com/cran/cSEM
Date/Publication: 2022-11-24 17:50:05 UTC
Number of recursive dependencies: 129

Run revdep_details(, "cSEM") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rdpack’ All declared Imports should be used.

cytomapper

Version: 1.14.0
GitHub: https://github.com/BodenmillerGroup/cytomapper
Source code: https://github.com/cran/cytomapper
Date/Publication: 2023-10-24
Number of recursive dependencies: 163

Run revdep_details(, "cytomapper") for more info

checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: R 1.3Mb doc 5.0Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘CATALYST’

DCATS

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/DCATS
Date/Publication: 2023-10-24
Number of recursive dependencies: 208

Run revdep_details(, "DCATS") for more info

checking package subdirectories ... NOTE Found the following CITATION file in a non-standard place: CITATION.cff Most likely ‘inst/CITATION’ should be used instead.
checking R code for possible problems ... NOTE svm_simMat: no visible binding for global variable ‘clusterRes’ Undefined global functions or variables: clusterRes

DeepBlueR

Version: 1.27.0
GitHub: NA
Source code: https://github.com/cran/DeepBlueR
Date/Publication: 2023-04-25
Number of recursive dependencies: 161

Run revdep_details(, "DeepBlueR") for more info

checking whether package ‘DeepBlueR’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeepBlueR/new/DeepBlueR.Rcheck/00install.out’ for details.

* installing *source* package ‘DeepBlueR’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
status 
 "503" 
Error in xml.rpc(deepblue_options("url"), "list_column_types", user_key) : 
  Problems
Error: unable to load R code in package ‘DeepBlueR’
Execution halted
ERROR: lazy loading failed for package ‘DeepBlueR’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeepBlueR/new/DeepBlueR.Rcheck/DeepBlueR’

* installing *source* package ‘DeepBlueR’ ...
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
status 
 "503" 
Error in xml.rpc(deepblue_options("url"), "list_column_types", user_key) : 
  Problems
Error: unable to load R code in package ‘DeepBlueR’
Execution halted
ERROR: lazy loading failed for package ‘DeepBlueR’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeepBlueR/old/DeepBlueR.Rcheck/DeepBlueR’

DelayedMatrixStats

Version: 1.24.0
GitHub: https://github.com/PeteHaitch/DelayedMatrixStats
Source code: https://github.com/cran/DelayedMatrixStats
Date/Publication: 2023-10-24
Number of recursive dependencies: 76

Run revdep_details(, "DelayedMatrixStats") for more info

checking dependencies in R code ... NOTE Missing object imported by a ':::' call: ‘DelayedArray:::.reduce_array_dimensions’ Unexported objects imported by ':::' calls: ‘DelayedArray:::.get_ans_type’ ‘DelayedArray:::BLOCK_colVars’ ‘DelayedArray:::BLOCK_rowVars’ ‘DelayedArray:::RleArraySeed’ ‘DelayedArray:::get_Nindex_lengths’ ‘DelayedArray:::set_dim’ ‘DelayedArray:::set_dimnames’ ‘DelayedArray:::subset_by_Nindex’ ‘DelayedArray:::to_linear_index’ See the note in ?`:::` about the use of this operator.

DELocal

Version: 1.2.0
GitHub: https://github.com/dasroy/DELocal
Source code: https://github.com/cran/DELocal
Date/Publication: 2023-10-24
Number of recursive dependencies: 176

Run revdep_details(, "DELocal") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘DELocal.Rmd’ using rmarkdown

Quitting from lines 78-85 [unnamed-chunk-5] (DELocal.Rmd) Error: processing vignette 'DELocal.Rmd' failed with diagnostics: Multiple cache results found. Please clear your cache by running biomartCacheClear() --- failed re-building ‘DELocal.Rmd’

SUMMARY: processing the following file failed: ‘DELocal.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: extdata 8.5Mb

DeMixT

Version: 1.16.0
GitHub: NA
Source code: https://github.com/cran/DeMixT
Date/Publication: 2023-04-25
Number of recursive dependencies: 138

Run revdep_details(, "DeMixT") for more info

checking whether package ‘DeMixT’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/DeMixT/new/DeMixT.Rcheck/00install.out’ for details.
checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'detect_suspicious_sample_by_hierarchical_clustering_2comp' ‘labels’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth', 'matrixcalc', 'rmarkdown', 'DSS', 'dendextend', 'psych', 'sva' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: data 1.9Mb libs 3.7Mb
checking R code for possible problems ... NOTE DeMixT_GS: no visible global function definition for ‘qchisq’ DeMixT_preprocessing: no visible global function definition for ‘quantile_normalization’ detect_suspicious_sample_by_hierarchical_clustering_2comp : <anonymous>: no visible global function definition for ‘wilcox.test’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘prcomp’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘dist’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible ... Undefined global functions or variables: DataFrame SimpleList abline as.dendrogram dist hclust legend median par points prcomp qchisq quantile_normalization rainbow segments wilcox.test Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "legend", "par", "points", "segments") importFrom("stats", "as.dendrogram", "dist", "hclust", "median", "prcomp", "qchisq", "wilcox.test") to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘calibrate’

DepecheR

Version: 1.18.0
GitHub: NA
Source code: https://github.com/cran/DepecheR
Date/Publication: 2023-10-24
Number of recursive dependencies: 120

Run revdep_details(, "DepecheR") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking compiled code ... NOTE ``` File ‘DepecheR/libs/DepecheR.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘Clusterer.o’ Found ‘srand’, possibly from ‘srand’ (C) Objects: ‘Clusterer.o’, ‘InterfaceUtils.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

DEqMS

Version: 1.20.0
GitHub: https://github.com/yafeng/DEqMS
Source code: https://github.com/cran/DEqMS
Date/Publication: 2023-10-24
Number of recursive dependencies: 118

Run revdep_details(, "DEqMS") for more info

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘matrixStats’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

DESeq2

Version: 1.42.0
GitHub: https://github.com/thelovelab/DESeq2
Source code: https://github.com/cran/DESeq2
Date/Publication: 2023-10-24
Number of recursive dependencies: 200

Run revdep_details(, "DESeq2") for more info

checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: doc 2.4Mb libs 4.2Mb

detrendr

Version: 0.6.15
GitHub: https://github.com/rorynolan/detrendr
Source code: https://github.com/cran/detrendr
Date/Publication: 2023-03-04 21:20:02 UTC
Number of recursive dependencies: 117

Run revdep_details(, "detrendr") for more info

checking installed package size ... NOTE installed size is 10.2Mb sub-directories of 1Mb or more: libs 9.2Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

DHS.rates

Version: 0.9.1
GitHub: NA
Source code: https://github.com/cran/DHS.rates
Date/Publication: 2021-12-09 19:00:02 UTC
Number of recursive dependencies: 65

Run revdep_details(, "DHS.rates") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rlang’ All declared Imports should be used.

diffUTR

Version: 1.10.0
GitHub: https://github.com/ETHZ-INS/diffUTR
Source code: https://github.com/cran/diffUTR
Date/Publication: 2023-10-24
Number of recursive dependencies: 150

Run revdep_details(, "diffUTR") for more info

checking R code for possible problems ... NOTE deuBinPlot: no visible binding for global variable 'x_start' deuBinPlot: no visible binding for global variable 'x_end' deuBinPlot: no visible binding for global variable 'y_start' deuBinPlot: no visible binding for global variable 'y_end' plotTopGenes: no visible binding for global variable 'sizeScore' plotTopGenes: no visible binding for global variable 'q.value' plotTopGenes: no visible binding for global variable 'density.ratio' plotTopGenes: no visible binding for global variable 'geneMeanDensity' plotTopGenes: no visible binding for global variable 'w.abs.coef' plotTopGenes: no visible binding for global variable 'tmp' plotTopGenes: no visible binding for global variable 'name' Undefined global functions or variables: density.ratio geneMeanDensity name q.value sizeScore tmp w.abs.coef x_end x_start y_end y_start
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘ggbio’

Dino

Version: 1.8.0
GitHub: https://github.com/JBrownBiostat/Dino
Source code: https://github.com/cran/Dino
Date/Publication: 2023-10-24
Number of recursive dependencies: 246

Run revdep_details(, "Dino") for more info

checking R code for possible problems ... NOTE checkCounts: no visible global function definition for ‘as’ Undefined global functions or variables: as Consider adding importFrom("methods", "as") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

disbayes

Version: 1.1.0
GitHub: https://github.com/chjackson/disbayes
Source code: https://github.com/cran/disbayes
Date/Publication: 2023-09-09 20:10:02 UTC
Number of recursive dependencies: 113

Run revdep_details(, "disbayes") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘disbayes.Rmd’ using rmarkdown

Quitting from lines 254-259 [unnamed-chunk-6] (disbayes.Rmd) Error: processing vignette 'disbayes.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘disbayes.Rmd’

SUMMARY: processing the following file failed: ‘disbayes.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 107.7Mb sub-directories of 1Mb or more: libs 107.0Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

DiscoRhythm

Version: 1.18.0
GitHub: https://github.com/matthewcarlucci/DiscoRhythm
Source code: https://github.com/cran/DiscoRhythm
Date/Publication: 2023-10-24
Number of recursive dependencies: 164

Run revdep_details(, "DiscoRhythm") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘data.table’ All declared Imports should be used.
checking R code for possible problems ... NOTE discoApp: no visible binding for global variable ‘.discorhythm_ncores’ discoApp: no visible binding for global variable ‘.discorhythm_local’ discoBatch: no visible binding for global variable ‘discoODAres’ Undefined global functions or variables: .discorhythm_local .discorhythm_ncores discoODAres
checking Rd files ... NOTE checkRd: (-1) discoParseMeta.Rd:28: Escaped LaTeX specials: \_ checkRd: (-1) discoParseMeta.Rd:29: Escaped LaTeX specials: \_

DMCFB

Version: 1.14.0
GitHub: https://github.com/shokoohi/DMCFB
Source code: https://github.com/cran/DMCFB
Date/Publication: 2023-05-07
Number of recursive dependencies: 118

Run revdep_details(, "DMCFB") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘DMCFB.Rmd’ using rmarkdown Error: processing vignette 'DMCFB.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘DMCFB.Rmd’

SUMMARY: processing the following file failed: ‘DMCFB.Rmd’

Error: Vignette re-building failed. Execution halted ```

dmrseq

Version: 1.22.0
GitHub: NA
Source code: https://github.com/cran/dmrseq
Date/Publication: 2023-10-24
Number of recursive dependencies: 169

Run revdep_details(, "dmrseq") for more info

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: data 4.8Mb doc 1.3Mb

Doscheda

Version: 1.24.0
GitHub: NA
Source code: https://github.com/cran/Doscheda
Date/Publication: 2023-10-24
Number of recursive dependencies: 153

Run revdep_details(, "Doscheda") for more info

checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: data 2.1Mb doc 1.6Mb shiny-examples 1.9Mb

DSWE

Version: 1.6.3
GitHub: https://github.com/TAMU-AML/DSWE-Package
Source code: https://github.com/cran/DSWE
Date/Publication: 2023-07-21 12:02:31 UTC
Number of recursive dependencies: 85

Run revdep_details(, "DSWE") for more info

checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: data 2.8Mb libs 4.8Mb

dwp

Version: 1.1
GitHub: NA
Source code: https://github.com/cran/dwp
Date/Publication: 2023-07-01 07:40:05 UTC
Number of recursive dependencies: 78

Run revdep_details(, "dwp") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘GenEst’ ‘expint’ ‘numDeriv’ All declared Imports should be used.

eaf

Version: 2.4.1
GitHub: https://github.com/MLopez-Ibanez/eaf
Source code: https://github.com/cran/eaf
Date/Publication: 2023-03-14 15:30:02 UTC
Number of recursive dependencies: 41

Run revdep_details(, "eaf") for more info

checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

easier

Version: 1.8.0
GitHub: NA
Source code: https://github.com/cran/easier
Date/Publication: 2023-10-24
Number of recursive dependencies: 198

Run revdep_details(, "easier") for more info

checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘reannotate_genes’
checking R code for possible problems ... NOTE compute_TF_activity: no visible binding for global variable ‘condition’ compute_TF_activity: no visible binding for global variable ‘score’ Undefined global functions or variables: condition score

ecospat

Version: 4.0.0
GitHub: https://github.com/ecospat/ecospat
Source code: https://github.com/cran/ecospat
Date/Publication: 2023-10-17 23:50:06 UTC
Number of recursive dependencies: 156

Run revdep_details(, "ecospat") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘vignette_ecospat_package.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'vignette_ecospat_package.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/ecospat/new/ecospat.Rcheck/vign_test/ecospat/vignettes/vignette_ecospat_package.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette_ecospat_package.log for more info. --- failed re-building ‘vignette_ecospat_package.Rmd’

SUMMARY: processing the following file failed: ‘vignette_ecospat_package.Rmd’

Error: Vignette re-building failed. Execution halted ```

EMDomics

Version: 2.32.0
GitHub: NA
Source code: https://github.com/cran/EMDomics
Date/Publication: 2023-10-24
Number of recursive dependencies: 46

Run revdep_details(, "EMDomics") for more info

checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Sadhika Malladi <contact@sadhikamalladi.com> [aut, cre] Daniel Schmolze <emd@schmolze.com> [aut, cre]
checking R code for possible problems ... NOTE .cvm_pairwise_q: no visible global function definition for ‘combn’ .cvm_pairwise_q : <anonymous>: no visible global function definition for ‘median’ .emd_gene_pairwise: no visible global function definition for ‘hist’ .emd_pairwise_q: no visible global function definition for ‘combn’ .emd_pairwise_q : <anonymous>: no visible global function definition for ‘median’ .ks_pairwise_table: no visible global function definition for ‘ks.test’ calculate_cvm: no visible global function definition for ‘combn’ calculate_cvm : <anonymous>: no visible global function definition for ... ‘median’ calculate_ks_gene: no visible global function definition for ‘combn’ calculate_ks_gene: no visible global function definition for ‘ks.test’ Undefined global functions or variables: combn hist ks.test median p.adjust Consider adding importFrom("graphics", "hist") importFrom("stats", "ks.test", "median", "p.adjust") importFrom("utils", "combn") to your NAMESPACE file.

ENmix

Version: 1.38.01
GitHub: https://github.com/Bioconductor/ENmix
Source code: https://github.com/cran/ENmix
Date/Publication: 2023-10-25
Number of recursive dependencies: 180

Run revdep_details(, "ENmix") for more info

checking installed package size ... NOTE installed size is 21.0Mb sub-directories of 1Mb or more: doc 2.3Mb

EnrichedHeatmap

Version: 1.32.0
GitHub: https://github.com/jokergoo/EnrichedHeatmap
Source code: https://github.com/cran/EnrichedHeatmap
Date/Publication: 2023-10-24
Number of recursive dependencies: 106

Run revdep_details(, "EnrichedHeatmap") for more info

checking installed package size ... NOTE installed size is 16.3Mb sub-directories of 1Mb or more: doc 13.3Mb extdata 1.6Mb libs 1.2Mb

EpiDISH

Version: 2.18.0
GitHub: https://github.com/sjczheng/EpiDISH
Source code: https://github.com/cran/EpiDISH
Date/Publication: 2023-10-24
Number of recursive dependencies: 92

Run revdep_details(, "EpiDISH") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

epimutacions

Version: 1.5.3
GitHub: https://github.com/isglobal-brge/epimutacions
Source code: https://github.com/cran/epimutacions
Date/Publication: 2023-05-30
Number of recursive dependencies: 249

Run revdep_details(, "epimutacions") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘epimutacions.Rmd’ using rmarkdown

Quitting from lines 610-611 [annot] (epimutacions.Rmd) Error: processing vignette 'epimutacions.Rmd' failed with diagnostics: Multiple cache results found. Please clear your cache by running biomartCacheClear() --- failed re-building ‘epimutacions.Rmd’

SUMMARY: processing the following file failed: ‘epimutacions.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘CompQuadForm’, ‘car’

epistasisGA

Version: 1.4.0
GitHub: https://github.com/mnodzenski/epistasisGA
Source code: https://github.com/cran/epistasisGA
Date/Publication: 2023-10-24
Number of recursive dependencies: 135

Run revdep_details(, "epistasisGA") for more info

checking installed package size ... NOTE installed size is 13.7Mb sub-directories of 1Mb or more: doc 4.0Mb libs 9.3Mb

eseis

Version: 0.7.3
GitHub: NA
Source code: https://github.com/cran/eseis
Date/Publication: 2023-08-10 14:00:03 UTC
Number of recursive dependencies: 69

Run revdep_details(, "eseis") for more info

checking startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector2” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector2” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```

evaluomeR

Version: 1.18.0
GitHub: https://github.com/neobernad/evaluomeR
Source code: https://github.com/cran/evaluomeR
Date/Publication: 2023-10-24
Number of recursive dependencies: 119

Run revdep_details(, "evaluomeR") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'SummarizedExperiment', 'MultiAssayExperiment', 'cluster', 'fpc', 'randomForest', 'flexmix' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘kableExtra’ All declared Imports should be used. Packages in Depends field not imported from: ‘flexmix’ ‘randomForest’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

EventPointer

Version: 3.10.0
GitHub: https://github.com/jpromeror/EventPointer
Source code: https://github.com/cran/EventPointer
Date/Publication: 2023-10-24
Number of recursive dependencies: 179

Run revdep_details(, "EventPointer") for more info

checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘SGSeq:::addFeatureID’ ‘SGSeq:::addGeneID’ ‘SGSeq:::edges’ ‘SGSeq:::exonGraph’ ‘SGSeq:::feature2name’ ‘SGSeq:::matchSGFeatures’ ‘SGSeq:::nodes’ ‘SGSeq:::propagateAnnotation’ ‘SGSeq:::splitCharacterList’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE EventDetection_transcriptome: no visible binding for global variable ‘jj’ SF_Prediction: no visible binding for global variable ‘valueRanking’ SF_Prediction: no visible binding for global variable ‘PSI_table’ annotate2: no visible global function definition for ‘addDummySpliceSites’ annotate2: no visible global function definition for ‘annotatePaths’ annotateFeatures2: no visible global function definition for ‘matchTxFeatures’ callGRseq_parallel: no visible global function definition for ... ‘stopCluster’ fitgl: no visible binding for global variable ‘hist’ myphyper: no visible global function definition for ‘dhyper’ Undefined global functions or variables: PSI_table addDummySpliceSites annotatePaths dhyper hist i ii jj makeCluster matchTxFeatures stopCluster valueRanking Consider adding importFrom("graphics", "hist") importFrom("stats", "dhyper") to your NAMESPACE file.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'InternalFunctions': ‘sort.exons’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

ExCluster

Version: 1.20.0
GitHub: NA
Source code: https://github.com/cran/ExCluster
Date/Publication: 2023-10-24
Number of recursive dependencies: 41

Run revdep_details(, "ExCluster") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

ExpHunterSuite

Version: 1.8.0
GitHub: NA
Source code: https://github.com/cran/ExpHunterSuite
Date/Publication: 2023-04-28
Number of recursive dependencies: 279

Run revdep_details(, "ExpHunterSuite") for more info

checking whether package ‘ExpHunterSuite’ can be installed ... ERROR Installation failed. See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ExpHunterSuite/new/ExpHunterSuite.Rcheck/00install.out’ for details.

* installing *source* package ‘ExpHunterSuite’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

Warning: namespace ‘ExpHunterSuite’ is not available and has been replaced
by .GlobalEnv when processing object ‘degh_output’
Warning: namespace ‘ExpHunterSuite’ is not available and has been replaced
by .GlobalEnv when processing object ‘degh_output’
...
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'HPO.db', details:
  call: NULL
  error: Corrupt Cache: index file
  See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
  cache: /c4/home/henrik/.cache/R/AnnotationHub
  filename: annotationhub.index.rds
Execution halted
ERROR: lazy loading failed for package ‘ExpHunterSuite’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ExpHunterSuite/new/ExpHunterSuite.Rcheck/ExpHunterSuite’

* installing *source* package ‘ExpHunterSuite’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

Warning: namespace ‘ExpHunterSuite’ is not available and has been replaced
by .GlobalEnv when processing object ‘degh_output’
Warning: namespace ‘ExpHunterSuite’ is not available and has been replaced
by .GlobalEnv when processing object ‘degh_output’
...
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'HPO.db', details:
  call: NULL
  error: Corrupt Cache: index file
  See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
  cache: /c4/home/henrik/.cache/R/AnnotationHub
  filename: annotationhub.index.rds
Execution halted
ERROR: lazy loading failed for package ‘ExpHunterSuite’
* removing ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ExpHunterSuite/old/ExpHunterSuite.Rcheck/ExpHunterSuite’

ExpressionNormalizationWorkflow

Version: 1.28.0
GitHub: https://github.com/NA/NA
Source code: https://github.com/cran/ExpressionNormalizationWorkflow
Date/Publication: 2023-10-25
Number of recursive dependencies: 129

Run revdep_details(, "ExpressionNormalizationWorkflow") for more info

checking whether package ‘ExpressionNormalizationWorkflow’ can be installed ... WARNING Found the following significant warnings: Warning: ExpressionNormalizationWorkflow-package.Rd:29: All text must be in a section Warning: ExpressionNormalizationWorkflow-package.Rd:30: All text must be in a section Warning: replacing previous import ‘Biobase::rowMedians’ by ‘matrixStats::rowMedians’ when loading ‘ExpressionNormalizationWorkflow’ Warning: replacing previous import ‘Biobase::anyMissing’ by ‘matrixStats::anyMissing’ when loading ‘ExpressionNormalizationWorkflow’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ExpressionNormalizationWorkflow/new/ExpressionNormalizationWorkflow.Rcheck/00install.out’ for details.
checking Rd files ... WARNING prepare_Rd: ExpressionNormalizationWorkflow-package.Rd:29: All text must be in a section prepare_Rd: ExpressionNormalizationWorkflow-package.Rd:30: All text must be in a section
checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: doc 2.5Mb extdata 4.7Mb
checking R code for possible problems ... NOTE expSetobj: no visible global function definition for ‘new’ pvcAnaly: no visible global function definition for ‘barplot’ pvcAnaly: no visible global function definition for ‘axis’ pvcAnaly: no visible global function definition for ‘text’ pvcaBatchAssess: no visible global function definition for ‘cor’ pvcaBatchAssess: no visible binding for global variable ‘na.omit’ pvcaBatchAssess: no visible global function definition for ‘sigma’ snmAnaly: no visible global function definition for ‘model.matrix’ snmAnaly: no visible global function definition for ‘write.table’ surVarAnaly: no visible global function definition for ‘model.matrix’ Undefined global functions or variables: axis barplot cor model.matrix na.omit new sigma text write.table Consider adding importFrom("graphics", "axis", "barplot", "text") importFrom("methods", "new") importFrom("stats", "cor", "model.matrix", "na.omit", "sigma") importFrom("utils", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking Rd cross-references ... NOTE Unknown package ‘<pkg>’ in Rd xrefs
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocManager’

extraChIPs

Version: 1.6.0
GitHub: https://github.com/smped/extraChIPs
Source code: https://github.com/cran/extraChIPs
Date/Publication: 2023-10-24
Number of recursive dependencies: 257

Run revdep_details(, "extraChIPs") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocParallel', 'GenomicRanges', 'ggplot2', 'ggside', 'SummarizedExperiment', 'tibble' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

FastPCS

Version: 0.1.3
GitHub: NA
Source code: https://github.com/cran/FastPCS
Date/Publication: 2018-05-22 16:49:12 UTC
Number of recursive dependencies: 6

Run revdep_details(, "FastPCS") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 11.4Mb sub-directories of 1Mb or more: libs 11.4Mb
checking Rd files ... NOTE checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \& checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&

FastRCS

Version: 0.0.8
GitHub: NA
Source code: https://github.com/cran/FastRCS
Date/Publication: 2018-05-13 19:59:51 UTC
Number of recursive dependencies: 6

Run revdep_details(, "FastRCS") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 23.5Mb sub-directories of 1Mb or more: libs 23.4Mb
checking Rd files ... NOTE checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \& checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&

fastverse

Version: 0.3.2
GitHub: https://github.com/fastverse/fastverse
Source code: https://github.com/cran/fastverse
Date/Publication: 2023-09-20 07:20:06 UTC
Number of recursive dependencies: 58

Run revdep_details(, "fastverse") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’ All declared Imports should be used.

FDb.FANTOM4.promoters.hg19

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/FDb.FANTOM4.promoters.hg19
Number of recursive dependencies: 92

Run revdep_details(, "FDb.FANTOM4.promoters.hg19") for more info

checking package subdirectories ... WARNING Found the following non-empty subdirectories of ‘inst’ also used by R: inst/build It is recommended not to interfere with package subdirectories used by R.
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘GenomicFeatures’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘BSgenome.Hsapiens.UCSC.hg19’ ‘matrixStats’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘Biostrings’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘matrixStats:::rowProds’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE oecg: no visible global function definition for ‘is’ oecg: no visible global function definition for ‘seqlengths’ oecg: no visible binding for global variable ‘Hsapiens’ oecg: no visible global function definition for ‘seqlevels’ oecg: no visible global function definition for ‘seqnames’ oecg: no visible global function definition for ‘resize’ oecg: no visible global function definition for ‘start’ oecg: no visible global function definition for ‘start<-’ oecg: no visible global function definition for ‘end’ oecg: no visible global function definition for ‘end<-’ ... oecg: no visible global function definition for ‘letterFrequency’ oecg: no visible global function definition for ‘dinucleotideFrequency’ Undefined global functions or variables: Hsapiens dinucleotideFrequency end end<- getSeq is letterFrequency resize seqlengths seqlevels seqnames start start<- width Consider adding importFrom("methods", "is") importFrom("stats", "end", "start") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

FEAST

Version: 1.10.0
GitHub: https://github.com/suke18/FEAST
Source code: https://github.com/cran/FEAST
Date/Publication: 2023-10-24
Number of recursive dependencies: 222

Run revdep_details(, "FEAST") for more info

checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: data 3.9Mb doc 1.3Mb
checking R code for possible problems ... NOTE FEAST: multiple local function definitions for ‘bp_fun’ with different formal arguments SC3_Clust: no visible global function definition for ‘metadata’ Visual_Rslt: no visible global function definition for ‘ggbarplot’ Visual_Rslt: no visible global function definition for ‘theme’ Visual_Rslt: no visible global function definition for ‘element_text’ Visual_Rslt: no visible global function definition for ‘ggline’ Visual_Rslt: no visible global function definition for ‘get_palette’ Visual_Rslt: no visible global function definition for ‘scale_y_continuous’ Visual_Rslt: no visible global function definition for ‘guides’ Visual_Rslt: no visible global function definition for ‘guide_legend’ Visual_Rslt: no visible global function definition for ‘ggarrange’ aricode_NMI : entropy: no visible global function definition for ‘sortPairs’ Undefined global functions or variables: element_text get_palette ggarrange ggbarplot ggline guide_legend guides metadata scale_y_continuous sortPairs theme

fipp

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/fipp
Date/Publication: 2021-02-11 10:30:02 UTC
Number of recursive dependencies: 34

Run revdep_details(, "fipp") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

fishpond

Version: 2.8.0
GitHub: NA
Source code: https://github.com/cran/fishpond
Date/Publication: 2023-10-24
Number of recursive dependencies: 204

Run revdep_details(, "fishpond") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘allelic.Rmd’ using rmarkdown

Quitting from lines 306-308 [unnamed-chunk-12] (allelic.Rmd) Error: processing vignette 'allelic.Rmd' failed with diagnostics: unable to find FTP dir for assembly GCF_000001405.40 in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/ --- failed re-building ‘allelic.Rmd’

--- re-building ‘swish.Rmd’ using rmarkdown --- finished re-building ‘swish.Rmd’

SUMMARY: processing the following file failed: ‘allelic.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: doc 5.0Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'samr:::localfdr' 'samr:::predictlocalfdr' 'samr:::qvalue.func' 'samr:::samr.compute.delta.table.seq' See the note in ?`:::` about the use of this operator.

flowCore

Version: 2.14.0
GitHub: NA
Source code: https://github.com/cran/flowCore
Date/Publication: 2023-10-24
Number of recursive dependencies: 123

Run revdep_details(, "flowCore") for more info

checking for missing documentation entries ... WARNING Undocumented code objects: ‘multiRangeGate’ Undocumented S4 classes: ‘multiRangeGate’ Undocumented S4 methods: generic '%in%' and siglist 'flowFrame,multiRangeGate' generic 'show' and siglist 'multiRangeGate' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking compiled code ... WARNING ``` File ‘flowCore/libs/flowCore.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Object: ‘fcsTextParse.o’ Found ‘sprintf’, possibly from ‘sprintf’ (C) Object: ‘Logicle.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘HowTo-flowCore.Rnw’ using knitr Error: processing vignette 'HowTo-flowCore.Rnw' failed with diagnostics: Running 'texi2dvi' on 'HowTo-flowCore.tex' failed. LaTeX errors: ! LaTeX Error: Filecomment.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.65 \usepackage {graphicx}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘HowTo-flowCore.Rnw’

SUMMARY: processing the following file failed: ‘HowTo-flowCore.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 17.9Mb sub-directories of 1Mb or more: R 1.1Mb data 5.4Mb extdata 1.1Mb libs 9.0Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) identifier-methods.Rd:36: Escaped LaTeX specials: \^ checkRd: (-1) quadraticTransform.Rd:26: Escaped LaTeX specials: \^ checkRd: (-1) read.FCS.Rd:26: Escaped LaTeX specials: \$

flowGraph

Version: 1.10.0
GitHub: https://github.com/aya49/flowGraph
Source code: https://github.com/cran/flowGraph
Date/Publication: 2023-10-24
Number of recursive dependencies: 95

Run revdep_details(, "flowGraph") for more info

checking R code for possible problems ... NOTE get_child: no visible binding for global variable ‘no_cores’ get_paren: no visible binding for global variable ‘no_cores’ ms_psig: no visible binding for global variable ‘meta’ Undefined global functions or variables: meta no_cores
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘doParallel’

flowWorkspace

Version: 4.14.0
GitHub: NA
Source code: https://github.com/cran/flowWorkspace
Date/Publication: 2023-10-24
Number of recursive dependencies: 112

Run revdep_details(, "flowWorkspace") for more info

checking Rd cross-references ... WARNING ``` Package unavailable to check Rd xrefs: ‘flowStats’ Missing link or links in documentation object 'gs_plot_pop_count_cv.Rd': ‘barchart’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking for missing documentation entries ... WARNING Undocumented code objects: ‘gs_clone’ ‘gs_copy_tree_only’ Undocumented S4 methods: generic 'dimnames' and siglist 'cytoframe' generic 'rownames' and siglist 'cytoframe' generic 'rownames<-' and siglist 'cytoframe' generic 'show' and siglist 'cytoframe' generic 'transform' and siglist 'cytoframe' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking Rd \usage sections ... WARNING ``` Documented arguments not in \usage in documentation object 'GatingSet-methods': ‘...’

Undocumented arguments in documentation object 'convert' ‘backend’

Undocumented arguments in documentation object 'cs_get_uri' ‘x’

Undocumented arguments in documentation object 'gh_apply_to_new_fcs' ... ‘backend’ ‘backend_dir’

Undocumented arguments in documentation object 'save_gs' ‘cdf’ ‘backend_readonly’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking compilation flags in Makevars ... WARNING Non-portable flags in variable 'PKG_CPPFLAGS': -Wno-pedantic
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 73.0Mb sub-directories of 1Mb or more: doc 3.5Mb libs 68.2Mb
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Non-standard license specification: AGPL-3.0-only Standardizable: FALSE
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RBGL’ ‘RProtoBufLib’ ‘ggplot2’ ‘grDevices’ ‘graphics’ ‘utils’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘DelayedArray:::simplify_NULL_dimnames’ ‘flowCore:::.estimateLogicle’ ‘flowCore:::.spillover_pattern’ ‘flowCore:::checkClass’ ‘flowCore:::guid’ ‘flowCore:::logicle_transform’ ‘flowCore:::parse_pd_for_read_fs’ ‘flowCore:::txt2spillmatrix’ ‘flowCore:::updateTransformKeywords’ ‘flowCore:::validFilterResultList’ ‘graph:::.makeEdgeKeys’ ‘ncdfFlow:::.isValidSamples’ ‘stats:::.splinefun’ See the note in ?`:::` about the use of this operator.
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.
checking compiled code ... NOTE ``` File ‘flowWorkspace/libs/flowWorkspace.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Objects: ‘R_GatingSet.o’, ‘cytoframeAPI.o’, ‘cytosetAPI.o’ Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘R_GatingSet.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

footBayes

Version: 0.2.0
GitHub: https://github.com/leoegidi/footbayes
Source code: https://github.com/cran/footBayes
Date/Publication: 2023-08-31 14:50:02 UTC
Number of recursive dependencies: 147

Run revdep_details(, "footBayes") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tidyverse’ All declared Imports should be used.

FRASER

Version: 1.14.0
GitHub: https://github.com/gagneurlab/FRASER
Source code: https://github.com/cran/FRASER
Date/Publication: 2023-10-24
Number of recursive dependencies: 190

Run revdep_details(, "FRASER") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘FRASER.Rnw’ using knitr The magick package is required to crop "figure/quick_fraser_guide-1.png" but not available. The magick package is required to crop "figure/filter_junctions-1.png" but not available. The magick package is required to crop "figure/sample_covariation-1.png" but not available. The magick package is required to crop "figure/covariation_after_fitting-1.png" but not available. The magick package is required to crop "figure/finding_candidates-1.png" but not available. The magick package is required to crop "figure/figure_findBestQ-1.png" but not available. The magick package is required to crop "figure/result_visualization-1.png" but not available. The magick package is required to crop "figure/result_visualization-2.png" but not available. ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘FRASER.Rnw’

SUMMARY: processing the following file failed: ‘FRASER.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 9.6Mb sub-directories of 1Mb or more: R 1.3Mb doc 1.6Mb libs 5.9Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’ See the note in ?`:::` about the use of this operator.

funtooNorm

Version: 1.26.0
GitHub: NA
Source code: https://github.com/cran/funtooNorm
Date/Publication: 2023-10-24
Number of recursive dependencies: 153

Run revdep_details(, "funtooNorm") for more info

checking Rd \usage sections ... WARNING ``` Documented arguments not in \usage in documentation object 'show,SampleSet-method': ‘...’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘MyEndnoteLibrary.bib’ ‘funtooNorm.Rmd’ ‘funtooNorm.pdf’ ‘validationcurvesPCRlow.jpg’ Files named as vignettes but with no recognized vignette engine: ‘vignettes/funtooNorm.Rmd’ (Is a VignetteBuilder field missing?)

gap

Version: 1.5-3
GitHub: https://github.com/jinghuazhao/R
Source code: https://github.com/cran/gap
Date/Publication: 2023-08-26 14:10:07 UTC
Number of recursive dependencies: 179

Run revdep_details(, "gap") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘shiny’
checking installed package size ... NOTE installed size is 9.4Mb sub-directories of 1Mb or more: doc 7.9Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘car’

geneticae

Version: 0.4.0
GitHub: https://github.com/jangelini/geneticae
Source code: https://github.com/cran/geneticae
Date/Publication: 2022-07-20 15:40:06 UTC
Number of recursive dependencies: 155

Run revdep_details(, "geneticae") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’ ‘reshape2’ All declared Imports should be used.

GeneTonic

Version: 2.6.0
GitHub: https://github.com/federicomarini/GeneTonic
Source code: https://github.com/cran/GeneTonic
Date/Publication: 2023-10-24
Number of recursive dependencies: 214

Run revdep_details(, "GeneTonic") for more info

checking installed package size ... NOTE installed size is 17.4Mb sub-directories of 1Mb or more: data 1.2Mb doc 14.0Mb extdata 1.4Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘pcaExplorer’

genomation

Version: 1.34.0
GitHub: https://github.com/BIMSBbioinfo/genomation
Source code: https://github.com/cran/genomation
Date/Publication: 2023-10-24
Number of recursive dependencies: 111

Run revdep_details(, "genomation") for more info

checking whether package ‘genomation’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/genomation/new/genomation.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: doc 3.5Mb extdata 1.2Mb libs 2.0Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ScoreMatrixBin,RleList-GRangesList: no visible binding for global variable ‘id’ ScoreMatrixBin,RleList-GRangesList: no visible global function definition for ‘:=’ Undefined global functions or variables: := id

geocmeans

Version: 0.3.4
GitHub: https://github.com/JeremyGelb/geocmeans
Source code: https://github.com/cran/geocmeans
Date/Publication: 2023-09-12 03:10:02 UTC
Number of recursive dependencies: 198

Run revdep_details(, "geocmeans") for more info

checking installed package size ... NOTE installed size is 13.5Mb sub-directories of 1Mb or more: extdata 3.0Mb libs 8.2Mb

geva

Version: 1.10.0
GitHub: https://github.com/sbcblab/geva
Source code: https://github.com/cran/geva
Date/Publication: 2023-10-24
Number of recursive dependencies: 126

Run revdep_details(, "geva") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: ... --- re-building ‘geva.Rmd’ using rmarkdown Warning in Sys.setlocale("LC_TIME", "English_United States") : OS reports request to set locale to "English_United States" cannot be honored The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-summary-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-quantiles-1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-quantiles-2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-cluster-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva_files/figure-latex/plot-geva-cluster-grouped-1.png" but not available. ...

Error: processing vignette 'geva.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/geva/new/geva.Rcheck/vign_test/geva/vignettes/geva.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See geva.log for more info. --- failed re-building ‘geva.Rmd’

SUMMARY: processing the following file failed: ‘geva.Rmd’

Error: Vignette re-building failed. Execution halted ```

ggdmc

Version: 0.2.6.0
GitHub: https://github.com/yxlin/ggdmc
Source code: https://github.com/cran/ggdmc
Date/Publication: 2019-04-29 05:10:03 UTC
Number of recursive dependencies: 53

Run revdep_details(, "ggdmc") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: libs 9.0Mb
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

GGPA

Version: 1.14.0
GitHub: https://github.com/dongjunchung/GGPA
Source code: https://github.com/cran/GGPA
Date/Publication: 2023-10-24
Number of recursive dependencies: 76

Run revdep_details(, "GGPA") for more info

checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: doc 1.6Mb libs 4.7Mb
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘network’ ‘scales’ ‘sna’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking compiled code ... NOTE ``` File ‘GGPA/libs/GGPA.so’: Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘3_Param.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

GJRM

Version: 0.2-6.4
GitHub: NA
Source code: https://github.com/cran/GJRM
Date/Publication: 2023-06-21 18:50:02 UTC
Number of recursive dependencies: 60

Run revdep_details(, "GJRM") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘sp’

glmGamPoi

Version: 1.14.0
GitHub: https://github.com/const-ae/glmGamPoi
Source code: https://github.com/cran/glmGamPoi
Date/Publication: 2023-10-24
Number of recursive dependencies: 169

Run revdep_details(, "glmGamPoi") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 14.0Mb sub-directories of 1Mb or more: doc 2.4Mb libs 11.2Mb

GPUmatrix

Version: 0.1.1
GitHub: NA
Source code: https://github.com/cran/GPUmatrix
Date/Publication: 2023-10-16 18:30:07 UTC
Number of recursive dependencies: 59

Run revdep_details(, "GPUmatrix") for more info

checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'gpu.matrix.Rd': ‘Matrix-class’

Missing link or links in documentation object 'matrix-product.Rd': ‘%&%’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```

GRaNIE

Version: 1.6.1
GitHub: NA
Source code: https://github.com/cran/GRaNIE
Date/Publication: 2023-10-26
Number of recursive dependencies: 311

Run revdep_details(, "GRaNIE") for more info

checking installed package size ... NOTE installed size is 12.8Mb sub-directories of 1Mb or more: doc 11.6Mb
checking R code for possible problems ... NOTE .performIHW: no visible binding for global variable 'adj_pvalue' Undefined global functions or variables: adj_pvalue

graper

Version: 1.18.0
GitHub: NA
Source code: https://github.com/cran/graper
Date/Publication: 2023-10-24
Number of recursive dependencies: 75

Run revdep_details(, "graper") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: doc 1.8Mb libs 7.1Mb

GUIDEseq

Version: 1.32.0
GitHub: NA
Source code: https://github.com/cran/GUIDEseq
Date/Publication: 2023-10-24
Number of recursive dependencies: 197

Run revdep_details(, "GUIDEseq") for more info

checking installed package size ... NOTE installed size is 12.5Mb sub-directories of 1Mb or more: extdata 11.9Mb
checking dependencies in R code ... NOTE ':::' call which should be '::': ‘CRISPRseek:::translatePattern’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE plotTracks: warning in scale_x_continuous(label = xaxis.lab.pos$chromosome, breaks = xaxis.lab.pos$chr.center): partial argument match of 'label' to 'labels' .maskSubSeq: no visible global function definition for ‘.getMatchedInd’ .nucleotideSubstitutionMatrix: no visible binding for global variable ‘IUPAC_CODE_MAP’ .nucleotideSubstitutionMatrix: no visible binding for global variable ‘DNA_BASES’ GUIDEseqAnalysis: no visible binding for global variable ‘offTarget’ GUIDEseqAnalysis: no visible binding for global variable ‘peak_score’ ... feature gRNA.deletion gRNA.insertion gRNA.name gRNAPlusPAM geom_smooth guideAlignment2OffTarget guide_legend guides h mismatch.distance2PAM n.DNA.bulge n.PAM.mismatch n.RNA.bulge n.deletion n.distinct.UMIs n.guide.mismatch n.insertion offTarget offTargetStrand offTarget_End offTarget_Start offTarget_sequence pa.f1 pa.r2 peak_score pos.deletion pos.insertion predicted_cleavage_score qwidth.first qwidth.last readName seqnames.first seqnames.last start.first start.last strand.first strand.last thePeak total.mismatch.bulge unit width.first width.last y
checking Rd files ... NOTE prepare_Rd: annotateOffTargets.Rd:35-37: Dropping empty section \details prepare_Rd: annotateOffTargets.Rd:63-65: Dropping empty section \references prepare_Rd: createBarcodeFasta.Rd:56-58: Dropping empty section \references prepare_Rd: getUsedBarcodes.Rd:53-55: Dropping empty section \references checkRd: (-1) mergePlusMinusPeaks.Rd:72: Escaped LaTeX specials: \_
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘GUIDEseq.Rnw’ using Sweave Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘GUIDEseq.Rnw’

SUMMARY: processing the following file failed: ‘GUIDEseq.Rnw’

Error: Vignette re-building failed. Execution halted ```

Gviz

Version: 1.46.0
GitHub: https://github.com/ivanek/Gviz
Source code: https://github.com/cran/Gviz
Date/Publication: 2023-10-24
Number of recursive dependencies: 162

Run revdep_details(, "Gviz") for more info

checking installed package size ... NOTE installed size is 9.8Mb sub-directories of 1Mb or more: R 1.7Mb doc 4.8Mb extdata 2.5Mb

GWENA

Version: 1.12.0
GitHub: https://github.com/Kumquatum/GWENA
Source code: https://github.com/cran/GWENA
Date/Publication: 2023-10-24
Number of recursive dependencies: 150

Run revdep_details(, "GWENA") for more info

checking whether package ‘GWENA’ can be installed ... WARNING Found the following significant warnings: Warning: bad markup (extra space?) at compare_conditions.Rd:91:72 Warning: bad markup (extra space?) at compare_conditions.Rd:96:77 Warning: bad markup (extra space?) at compare_conditions.Rd:98:74 Warning: bad markup (extra space?) at compare_conditions.Rd:100:69 See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/GWENA/new/GWENA.Rcheck/00install.out’ for details.
checking Rd files ... WARNING prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:91:72 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:96:77 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:98:74 prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:100:69
checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: data 2.3Mb doc 5.4Mb

HACSim

Version: 1.0.6-1
GitHub: NA
Source code: https://github.com/cran/HACSim
Date/Publication: 2022-06-13 06:50:16 UTC
Number of recursive dependencies: 38

Run revdep_details(, "HACSim") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: libs 1.9Mb shiny 4.2Mb

Harman

Version: 1.30.0
GitHub: NA
Source code: https://github.com/cran/Harman
Date/Publication: 2023-10-24
Number of recursive dependencies: 200

Run revdep_details(, "Harman") for more info

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: doc 2.8Mb libs 2.3Mb

hbamr

Version: 1.2.0
GitHub: https://github.com/jbolstad/hbamr
Source code: https://github.com/cran/hbamr
Date/Publication: 2023-09-25 15:00:02 UTC
Number of recursive dependencies: 83

Run revdep_details(, "hbamr") for more info

checking installed package size ... NOTE installed size is 319.0Mb sub-directories of 1Mb or more: libs 317.5Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

HDSpatialScan

Version: 1.0.4
GitHub: NA
Source code: https://github.com/cran/HDSpatialScan
Date/Publication: 2023-05-25 07:30:05 UTC
Number of recursive dependencies: 112

Run revdep_details(, "HDSpatialScan") for more info

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: libs 5.8Mb

hermes

Version: 1.6.0
GitHub: https://github.com/insightsengineering/hermes
Source code: https://github.com/cran/hermes
Date/Publication: 2023-10-24
Number of recursive dependencies: 164

Run revdep_details(, "hermes") for more info

checking tests ... ``` Running ‘test_dplyr_compatibility.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output:

══ Skipped tests (16) ══════════════════════════════════════════════════════════ • On CRAN (16): 'test-calc_cor.R:42:3', 'test-calc_cor.R:53:3', 'test-differential.R:122:3', 'test-differential.R:130:3', 'test-draw_barplot.R:11:3', 'test-draw_boxplot.R:12:3', ... ▆ 1. ├─hermes::query(genes(object), connection) at test-connections.R:171:2 2. └─hermes::query(genes(object), connection) 3. └─hermes::h_get_annotation_biomart(gene_ids, id_var = id_var, mart = mart) 4. └─biomaRt::getBM(...) 5. └─biomaRt:::.readFromCache(bfc, hash)

[ FAIL 4 | WARN 2 | SKIP 16 | PASS 831 ] Error: Test failures Execution halted ```

hipathia

Version: 3.2.0
GitHub: NA
Source code: https://github.com/cran/hipathia
Date/Publication: 2023-10-24
Number of recursive dependencies: 172

Run revdep_details(, "hipathia") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘hipathia-vignette.Rmd’ using rmarkdown ! LaTeX Error: Filetitling.sty' not found.

! Emergency stop.

Error: processing vignette 'hipathia-vignette.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/hipathia/new/hipathia.Rcheck/vign_test/hipathia/vignettes/hipathia-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See hipathia-vignette.log for more info. --- failed re-building ‘hipathia-vignette.Rmd’

SUMMARY: processing the following file failed: ‘hipathia-vignette.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 10.6Mb sub-directories of 1Mb or more: data 4.1Mb doc 1.8Mb extdata 4.4Mb
checking R code for possible problems ... NOTE DAreport: no visible binding for global variable ‘ID’ DAreport: no visible binding for global variable ‘FDRp.value’ DAtop : <anonymous>: no visible binding for global variable ‘FDRp.value’ DAtop : <anonymous>: no visible binding for global variable ‘statistic’ DAtop : <anonymous>: no visible binding for global variable ‘p.value’ DAtop : <anonymous>: no visible binding for global variable ‘name’ DAtop : <anonymous>: no visible binding for global variable ‘logPV’ DAtop : <anonymous>: no visible binding for global variable ‘feature’ DAtop: no visible binding for global variable ‘name’ ... summary_plot: no visible binding for global variable ‘UP.nodes’ summary_plot: no visible binding for global variable ‘DOWN.nodes’ summary_plot: no visible binding for global variable ‘nodes’ summary_plot: no visible binding for global variable ‘ratio.sigs’ summary_plot: no visible binding for global variable ‘ratio.UPs’ summary_plot: no visible binding for global variable ‘ratio.DOWNs’ Undefined global functions or variables: DOWN DOWN.nodes DOWNs FDRp.value ID Not UP UP.nodes UPs direction feature from functional logPV name nodes p.value ratio.DOWNs ratio.UPs ratio.sigs statistic status to total type value variable

iNETgrate

Version: 1.0.0
GitHub: https://github.com/Bioconductor/BiocManager
Source code: https://github.com/cran/iNETgrate
Date/Publication: 2023-10-24
Number of recursive dependencies: 295

Run revdep_details(, "iNETgrate") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘iNETgrate_inference.Rnw’ using knitr Error: processing vignette 'iNETgrate_inference.Rnw' failed with diagnostics: Running 'texi2dvi' on 'iNETgrate_inference.tex' failed. LaTeX errors: ! LaTeX Error: Filecommath.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.48 ^^M

! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘iNETgrate_inference.Rnw’

SUMMARY: processing the following file failed: ‘iNETgrate_inference.Rnw’

Error: Vignette re-building failed. Execution halted ```

InfiniumPurify

Version: 1.3.1
GitHub: NA
Source code: https://github.com/cran/InfiniumPurify
Date/Publication: 2017-01-14 12:12:25
Number of recursive dependencies: 1

Run revdep_details(, "InfiniumPurify") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘minfi’

IntOMICS

Version: 1.2.0
GitHub: https://github.com/anna-pacinkova/IntOMICS
Source code: https://github.com/cran/IntOMICS
Date/Publication: 2023-10-24
Number of recursive dependencies: 225

Run revdep_details(, "IntOMICS") for more info

checking data for ASCII and uncompressed saves ... WARNING Warning: package needs dependence on R (>= 2.10)

iPath

Version: 1.8.0
GitHub: https://github.com/suke18/iPath
Source code: https://github.com/cran/iPath
Date/Publication: 2023-10-24
Number of recursive dependencies: 132

Run revdep_details(, "iPath") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking R code for possible problems ... NOTE water_fall: no visible binding for global variable ‘value’ water_fall: no visible binding for global variable ‘type’ Undefined global functions or variables: type value

JMbayes2

Version: 0.4-5
GitHub: https://github.com/drizopoulos/JMbayes2
Source code: https://github.com/cran/JMbayes2
Date/Publication: 2023-06-26 13:30:05 UTC
Number of recursive dependencies: 80

Run revdep_details(, "JMbayes2") for more info

checking installed package size ... NOTE installed size is 11.6Mb sub-directories of 1Mb or more: libs 10.9Mb

kgschart

Version: 1.3.5
GitHub: https://github.com/kota7/kgschart
Source code: https://github.com/cran/kgschart
Date/Publication: 2017-07-02 22:16:15 UTC
Number of recursive dependencies: 76

Run revdep_details(, "kgschart") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

kissDE

Version: 1.20.0
GitHub: NA
Source code: https://github.com/cran/kissDE
Date/Publication: 2023-04-25
Number of recursive dependencies: 195

Run revdep_details(, "kissDE") for more info

checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘kissDE.rnw’ using Sweave Pre-processing the data... Trying to fit models on data... This can be a time-consuming step, so do not hesitate to have a look at the very well-written vignette ! Computing pvalues... Computing size of the effect and last cutoffs... Pre-processing the data... Trying to fit models on data... ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘kissDE.rnw’

SUMMARY: processing the following file failed: ‘kissDE.rnw’

Error: Vignette re-building failed. Execution halted ```

latrend

Version: 1.5.1
GitHub: https://github.com/philips-software/latrend
Source code: https://github.com/cran/latrend
Date/Publication: 2023-03-17 23:10:02 UTC
Number of recursive dependencies: 242

Run revdep_details(, "latrend") for more info

checking package dependencies ... NOTE Packages suggested but not available for checking: 'akmedoids', 'clusterCrit'
checking Rd cross-references ... NOTE Unknown packages ‘clusterCrit’, ‘akmedoids’ in Rd xrefs

ldsep

Version: 2.1.5
GitHub: https://github.com/dcgerard/ldsep
Source code: https://github.com/cran/ldsep
Date/Publication: 2022-10-18 22:52:43 UTC
Number of recursive dependencies: 175

Run revdep_details(, "ldsep") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: libs 8.3Mb

lemur

Version: 1.0.2
GitHub: https://github.com/const-ae/lemur
Source code: https://github.com/cran/lemur
Date/Publication: 2023-10-25
Number of recursive dependencies: 172

Run revdep_details(, "lemur") for more info

checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: data 2.6Mb doc 1.1Mb libs 2.6Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’ See the note in ?`:::` about the use of this operator.

LFDREmpiricalBayes

Version: 1.0
GitHub: NA
Source code: https://github.com/cran/LFDREmpiricalBayes
Date/Publication: 2017-09-27 09:08:46 UTC
Number of recursive dependencies: 35

Run revdep_details(, "LFDREmpiricalBayes") for more info

checking re-building of vignette outputs ... NOTE `` Error(s) in re-building vignettes: ... --- re-building ‘LFDREmpiricalBayes.Rnw’ using Sweave Error: processing vignette 'LFDREmpiricalBayes.Rnw' failed with diagnostics: Running 'texi2dvi' on 'LFDREmpiricalBayes.tex' failed. LaTeX errors: ! LaTeX Error: Filechangepage.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.10 \usepackage {url}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘LFDREmpiricalBayes.Rnw’

SUMMARY: processing the following file failed: ‘LFDREmpiricalBayes.Rnw’

Error: Vignette re-building failed. Execution halted ```

liger

Version: 2.0.1
GitHub: https://github.com/JEFworks/liger
Source code: https://github.com/cran/liger
Date/Publication: 2021-01-25 05:50:09 UTC
Number of recursive dependencies: 55

Run revdep_details(, "liger") for more info

checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: data 3.3Mb doc 2.1Mb libs 2.2Mb

Linnorm

Version: 2.26.0
GitHub: NA
Source code: https://github.com/cran/Linnorm
Date/Publication: 2023-10-24
Number of recursive dependencies: 108

Run revdep_details(, "Linnorm") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘Linnorm_User_Manual.Rmd’ using rmarkdown ! LaTeX Error: Filetitling.sty' not found.

! Emergency stop.

Error: processing vignette 'Linnorm_User_Manual.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/Linnorm/new/Linnorm.Rcheck/vign_test/Linnorm/vignettes/Linnorm_User_Manual.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Linnorm_User_Manual.log for more info. --- failed re-building ‘Linnorm_User_Manual.Rmd’

SUMMARY: processing the following file failed: ‘Linnorm_User_Manual.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 2.3Mb doc 1.9Mb libs 1.5Mb

LSAmitR

Version: 1.0-3
GitHub: NA
Source code: https://github.com/cran/LSAmitR
Date/Publication: 2022-06-01 07:50:02 UTC
Number of recursive dependencies: 164

Run revdep_details(, "LSAmitR") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘kerdiest’
checking data for non-ASCII characters ... NOTE Note: found 55 marked UTF-8 strings

lspartition

Version: 0.4
GitHub: NA
Source code: https://github.com/cran/lspartition
Date/Publication: 2019-08-08 22:40:06 UTC
Number of recursive dependencies: 34

Run revdep_details(, "lspartition") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

Luminescence

Version: 0.9.22
GitHub: https://github.com/R-Lum/Luminescence
Source code: https://github.com/cran/Luminescence
Date/Publication: 2023-08-07 14:30:02 UTC
Number of recursive dependencies: 150

Run revdep_details(, "Luminescence") for more info

checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: R 1.6Mb libs 3.5Mb

M3Drop

Version: 1.28.0
GitHub: https://github.com/tallulandrews/M3Drop
Source code: https://github.com/cran/M3Drop
Date/Publication: 2023-10-24
Number of recursive dependencies: 235

Run revdep_details(, "M3Drop") for more info

checking dependencies in R code ... WARNING Package in Depends field not imported from: ‘numDeriv’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Missing or unexported object: ‘scater::exprs’
checking installed package size ... NOTE installed size is 12.9Mb sub-directories of 1Mb or more: doc 12.6Mb
checking R code for possible problems ... NOTE M3DropConvertData: no visible global function definition for ‘assays’ NBumiConvertData: no visible global function definition for ‘assays’ bg__filter_cells: no visible binding for global variable ‘x’ bg__get_extreme_residuals: no visible binding for global variable ‘x’ Undefined global functions or variables: assays x
checking Rd files ... NOTE prepare_Rd: NBumi_FSOther.Rd:8-10: Dropping empty section \usage prepare_Rd: NBumi_TradDE.Rd:7-8: Dropping empty section \usage

maEndToEnd

Version: 2.22.0
GitHub: NA
Source code: https://github.com/cran/maEndToEnd
Date/Publication: 2023-10-25
Number of recursive dependencies: 264

Run revdep_details(, "maEndToEnd") for more info

checking DESCRIPTION meta-information ... WARNING Invalid license file pointers: LICENSE
checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'oligoClasses', 'ArrayExpress', 'pd.hugene.1.0.st.v1', 'hugene10sttranscriptcluster.db', 'oligo', 'arrayQualityMetrics', 'limma', 'topGO', 'ReactomePA', 'clusterProfiler', 'gplots', 'ggplot2', 'geneplotter', 'pheatmap', 'RColorBrewer', 'dplyr', 'tidyr', 'stringr', 'matrixStats', 'genefilter', 'openxlsx', 'Rgraphviz', 'enrichplot' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: doc 6.0Mb
checking top-level files ... NOTE File LICENCE is not mentioned in the DESCRIPTION file.
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘AnnotationDbi’

magpie

Version: 1.2.0
GitHub: https://github.com/dxd429/magpie
Source code: https://github.com/cran/magpie
Date/Publication: 2023-10-24
Number of recursive dependencies: 143

Run revdep_details(, "magpie") for more info

checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘htmltools’

MatrixGenerics

Version: 1.14.0
GitHub: https://github.com/Bioconductor/MatrixGenerics
Source code: https://github.com/cran/MatrixGenerics
Date/Publication: 2023-10-24
Number of recursive dependencies: 55

Run revdep_details(, "MatrixGenerics") for more info

checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘methods:::fromNextMethod’ ‘methods:::getGenericFromCall’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.load_next_suggested_package_to_search’

mcmcsae

Version: 0.7.5
GitHub: NA
Source code: https://github.com/cran/mcmcsae
Date/Publication: 2023-10-10 20:40:02 UTC
Number of recursive dependencies: 115

Run revdep_details(, "mcmcsae") for more info

checking installed package size ... NOTE installed size is 24.5Mb sub-directories of 1Mb or more: libs 23.2Mb

MEAL

Version: 1.32.0
GitHub: NA
Source code: https://github.com/cran/MEAL
Date/Publication: 2023-10-24
Number of recursive dependencies: 232

Run revdep_details(, "MEAL") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘MEAL.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 1-2.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Manhattan 2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Volcano 1-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/QQ-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Plot_Features-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/MEAL/new/MEAL.Rcheck/vign_test/MEAL/vignettes/MEAL_files/figure-html/Plot_Features-2.png" but not available.

... Quitting from lines 157-158 [Regional plot 2 exp] (caseExample.Rmd) Error: processing vignette 'caseExample.Rmd' failed with diagnostics: attempt to set an attribute on NULL --- failed re-building ‘caseExample.Rmd’

SUMMARY: processing the following files failed: ‘MEAL.Rmd’ ‘caseExample.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking dependencies in R code ... WARNING '::' or ':::' import not declared from: 'sva'
checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object 'getProbeResults' ‘robust’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking examples ... WARNING ``` Found the following significant warnings:

Warning: 'runRegionAnalysis' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE plotRegion: no visible global function definition for ‘subsetByOverlaps’ plotRegion: no visible global function definition for ‘mcols<-’ runRDA: no visible global function definition for ‘rowData’ runSVA: no visible global function definition for ‘resid’ runSVA: no visible global function definition for ‘quantile’ Undefined global functions or variables: mcols<- quantile resid rowData subsetByOverlaps Consider adding importFrom("stats", "quantile", "resid") to your NAMESPACE file.
checking Rd cross-references ... NOTE Unknown package ‘DMRcate’ in Rd xrefs

memes

Version: 1.10.0
GitHub: https://github.com/snystrom/memes
Source code: https://github.com/cran/memes
Date/Publication: 2023-10-24
Number of recursive dependencies: 162

Run revdep_details(, "memes") for more info

checking S3 generic/method consistency ... WARNING ``` motif_input: function(x, ...) motif_input.universalmotif_df: function(input, path)

motif_input: function(x, ...) motif_input.universalmotif: function(input, path)

... function(x) sequence_input.BStringSet: function(input)

sequence_input: function(x) sequence_input.AAStringSet: function(input) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. ```

metagene

Version: 2.31.0
GitHub: https://github.com/CharlesJB/metagene
Source code: https://github.com/cran/metagene
Date/Publication: 2022-11-01
Number of recursive dependencies: 132

Run revdep_details(, "metagene") for more info

checking tests ... ``` Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 50 lines of output: [1] TRUE produce data table : ChIP-Seq [1] TRUE produce data table : ChIP-Seq produce data table : ChIP-Seq ChIP-Seq flip/unflip ...
```
 test_parallel_job.R 
   test.parallel_job_get_core_count_valid_multiple_core_biocparallelparam 
   test.parallel_job_set_core_count_valid_multiple_core_biocparallelparam
```
Error in BiocGenerics:::testPackage("metagene") : unit tests failed for package metagene In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted ```
checking Rd files ... WARNING checkRd: (5) Bam_Handler.Rd:22: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:42: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:46: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:50: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:54: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:58: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:61-62: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:71-72: \item in \describe must have non-empty label checkRd: (5) Bam_Handler.Rd:81: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:23-26: \item in \describe must have non-empty label ... checkRd: (5) metagene.Rd:130: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:133: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:144: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:147: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:155: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:164: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:170: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:179: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:183: \item in \describe must have non-empty label checkRd: (5) metagene.Rd:186: \item in \describe must have non-empty label
checking installed package size ... NOTE installed size is 10.2Mb sub-directories of 1Mb or more: doc 3.2Mb extdata 5.3Mb
checking R code for possible problems ... NOTE NCIS.internal: no visible global function definition for 'est.norm.med.search' avoid_gaps_update: no visible binding for global variable 'value' avoid_gaps_update: no visible binding for global variable 'bam' avoid_gaps_update: no visible binding for global variable 'tab' avoid_gaps_update: no visible binding for global variable 'nuc' bin.data: no visible global function definition for 'hist' permutation_test: no visible global function definition for '.' permutation_test: no visible binding for global variable 'value' plot_metagene: no visible binding for global variable 'bin' ... plot_metagene: no visible binding for global variable 'group' plot_metagene: no visible binding for global variable 'nuc' plot_metagene: no visible binding for global variable 'design' plot_metagene: no visible binding for global variable 'nuctot' Undefined global functions or variables: . bam bin design est.norm.med.search group hist nuc nuctot qinf qsup tab value Consider adding importFrom("graphics", "hist") to your NAMESPACE file.

metagenomeSeq

Version: 1.43.0
GitHub: https://github.com/nosson/metagenomeSeq
Source code: https://github.com/cran/metagenomeSeq
Date/Publication: 2023-04-25
Number of recursive dependencies: 147

Run revdep_details(, "metagenomeSeq") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: > # but now you have the flexibility as requested by CRAN maintainers. > test_check("metagenomeSeq") Loading required package: metagenomeSeq Loading required package: Biobase Loading required package: BiocGenerics

... ── Failure ('test-norm.R:28:3'): cumNormStat returns the correct value ─────── cumNormStat(lungData) not equal to 0.7014946. names for target but not for current ── Failure ('test-norm.R:34:3'): cumNormStatFast returns the correct value ─── cumNormStatFast(lungData) not equal to 0.7014946. names for target but not for current

[ FAIL 2 | WARN 6 | SKIP 0 | PASS 13 ] Error: Test failures Execution halted ```

metamicrobiomeR

Version: 1.2
GitHub: https://github.com/nhanhocu/metamicrobiomeR
Source code: https://github.com/cran/metamicrobiomeR
Date/Publication: 2020-11-09 11:20:05 UTC
Number of recursive dependencies: 159

Run revdep_details(, "metamicrobiomeR") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘lmerTest’ All declared Imports should be used.

MetaNeighbor

Version: 1.22.0
GitHub: NA
Source code: https://github.com/cran/MetaNeighbor
Date/Publication: 2023-10-24
Number of recursive dependencies: 102

Run revdep_details(, "MetaNeighbor") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘MetaNeighbor.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'MetaNeighbor.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/MetaNeighbor/new/MetaNeighbor.Rcheck/vign_test/MetaNeighbor/vignettes/MetaNeighbor.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MetaNeighbor.log for more info. --- failed re-building ‘MetaNeighbor.Rmd’

SUMMARY: processing the following file failed: ‘MetaNeighbor.Rmd’

Error: Vignette re-building failed. Execution halted ```

MethReg

Version: 1.12.0
GitHub: https://github.com/TransBioInfoLab/MethReg
Source code: https://github.com/cran/MethReg
Date/Publication: 2023-10-24
Number of recursive dependencies: 228

Run revdep_details(, "MethReg") for more info

checking dependencies in R code ... WARNING Missing or unexported object: ‘downloader::download.file’
checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: R 1.6Mb doc 2.5Mb
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘downloader’ A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE readRemap2022: no visible binding for global variable ‘biotype’ Undefined global functions or variables: biotype
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘TCGAbiolinks’

methrix

Version: 1.16.0
GitHub: https://github.com/CompEpigen/methrix
Source code: https://github.com/cran/methrix
Date/Publication: 2023-10-24
Number of recursive dependencies: 166

Run revdep_details(, "methrix") for more info

checking R code for possible problems ... NOTE extract_CPGs: no visible global function definition for ‘standardChromosomes’ get_region_summary: no visible binding for global variable ‘..keep’ Undefined global functions or variables: ..keep standardChromosomes

MethylAid

Version: 1.36.0
GitHub: NA
Source code: https://github.com/cran/MethylAid
Date/Publication: 2023-10-24
Number of recursive dependencies: 177

Run revdep_details(, "MethylAid") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘MethylAid.Rnw’ using knitr Error: processing vignette 'MethylAid.Rnw' failed with diagnostics: Running 'texi2dvi' on 'MethylAid.tex' failed. LaTeX errors: ! LaTeX Error: Filenowidow.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘MethylAid.Rnw’

SUMMARY: processing the following file failed: ‘MethylAid.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘MethylAidData’

methylationArrayAnalysis

Version: 1.24.0
GitHub: NA
Source code: https://github.com/cran/methylationArrayAnalysis
Date/Publication: 2023-04-28
Number of recursive dependencies: 222

Run revdep_details(, "methylationArrayAnalysis") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: --- re-building ‘methylationArrayAnalysis.Rmd’ using rmarkdown The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure2-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure3-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure4-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure5-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure6-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure7-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure8-1.png" but not available. The magick package is required to crop "/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/vign_test/methylationArrayAnalysis/vignettes/methylationArrayAnalysis_files/figure-html/figure9-1.png" but not available. ...

trying URL 'https://cloud.r-project.org/src/contrib/readxl_1.4.3.tar.gz' Content type 'application/x-gzip' length 2093488 bytes (2.0 MB) ================================================== downloaded 2.0 MB

trying URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DMRcatedata_2.20.0.tar.gz' Content type 'application/x-gzip' length 105209 bytes (102 KB) ================================================== downloaded 102 KB ```
checking whether package ‘methylationArrayAnalysis’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'rmarkdown::pdf_document' by 'BiocStyle::pdf_document' when loading 'methylationArrayAnalysis' Warning: replacing previous import 'rmarkdown::html_document' by 'BiocStyle::html_document' when loading 'methylationArrayAnalysis' Warning: replacing previous import 'rmarkdown::md_document' by 'BiocStyle::md_document' when loading 'methylationArrayAnalysis' See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/methylationArrayAnalysis/new/methylationArrayAnalysis.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Depends: includes the non-default packages: 'knitr', 'rmarkdown', 'BiocStyle', 'limma', 'minfi', 'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'IlluminaHumanMethylation450kmanifest', 'RColorBrewer', 'missMethyl', 'matrixStats', 'minfiData', 'Gviz', 'DMRcate', 'stringr', 'FlowSorted.Blood.450k' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 322.7Mb sub-directories of 1Mb or more: doc 2.6Mb extdata 320.2Mb
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.

methylumi

Version: 2.48.0
GitHub: https://github.com/seandavi/methylumi
Source code: https://github.com/cran/methylumi
Date/Publication: 2023-10-24
Number of recursive dependencies: 168

Run revdep_details(, "methylumi") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'scales', 'reshape2', 'ggplot2', 'matrixStats', 'FDb.InfiniumMethylation.hg19', 'minfi' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 11.8Mb sub-directories of 1Mb or more: R 1.3Mb data 2.7Mb doc 1.9Mb extdata 5.8Mb
checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ ‘minfi’ ‘lattice’ ‘matrixStats’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘minfi’ ‘reshape2’ ‘scales’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘Biostrings’ ‘MASS’ ‘lumi’ ‘parallel’ ‘rtracklayer’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘graphics’ All declared Imports should be used. ... Packages in Depends field not imported from: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘methods’ ‘reshape2’ ‘scales’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘lumi:::produceMethylationGEOSubmissionFile’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘Biobase:::unsafeSetSlot’ ‘genefilter:::.findCentralMap’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE getBarcodes: warning in list.files(path = path, patt = "idat"): partial argument match of 'patt' to 'pattern' coerce,RangedSummarizedExperiment-GenomicMethylSet: warning in assays(from, withDim = F): partial argument match of 'withDim' to 'withDimnames' .getFinalReportBlock: no visible global function definition for ‘read.table’ .mclapply: no visible global function definition for ‘mclapply’ .parallel : <anonymous>: no visible global function definition for ‘ecdf’ ... subsetCommonProbes text theme_bw title value variable weighted.mean Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "abline", "axis", "box", "lines", "par", "points", "rect", "text", "title") importFrom("stats", "as.dist", "dnorm", "ecdf", "hclust", "offset", "p.adjust", "pnorm", "weighted.mean") importFrom("utils", "capture.output", "data", "packageDescription", "packageVersion", "read.csv", "read.delim", "read.table") to your NAMESPACE file.
checking Rd files ... NOTE prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples checkRd: (-1) extractBarcodeAndPosition.Rd:14: Escaped LaTeX specials: \_ \_
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

microbiomeExplorer

Version: 1.12.0
GitHub: NA
Source code: https://github.com/cran/microbiomeExplorer
Date/Publication: 2023-10-24
Number of recursive dependencies: 188

Run revdep_details(, "microbiomeExplorer") for more info

checking installed package size ... NOTE installed size is 12.5Mb sub-directories of 1Mb or more: doc 5.0Mb extdata 4.1Mb shiny 2.8Mb

MicrobiomeStat

Version: 1.1
GitHub: NA
Source code: https://github.com/cran/MicrobiomeStat
Date/Publication: 2022-01-24 00:02:41 UTC
Number of recursive dependencies: 107

Run revdep_details(, "MicrobiomeStat") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘MASS’ ‘Matrix’ ‘utils’ All declared Imports should be used.

microsamplingDesign

Version: 1.0.8
GitHub: NA
Source code: https://github.com/cran/microsamplingDesign
Date/Publication: 2021-10-13 13:52:04 UTC
Number of recursive dependencies: 140

Run revdep_details(, "microsamplingDesign") for more info

checking re-building of vignette outputs ... WARNING Error(s) in re-building vignettes: ... --- re-building ‘microsamplingDesign.Rmd’ using rmarkdown Warning: The closing backticks on line 165 ("") in microsamplingDesign.Rmd do not match the opening backticks " ``" on line 163. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'microsamplingDesign.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/microsamplingDesign/new/microsamplingDesign.Rcheck/vign_test/microsamplingDesign/vignettes/microsamplingDesign.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See microsamplingDesign.log for more info. --- failed re-building ‘microsamplingDesign.Rmd’

SUMMARY: processing the following file failed: ‘microsamplingDesign.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

migest

Version: 2.0.3
GitHub: https://github.com/guyabel/migest
Source code: https://github.com/cran/migest
Date/Publication: 2022-10-28 11:05:05 UTC
Number of recursive dependencies: 123

Run revdep_details(, "migest") for more info

checking data for non-ASCII characters ... NOTE Note: found 9 marked UTF-8 strings

miloR

Version: 1.10.0
GitHub: https://github.com/MarioniLab/miloR
Source code: https://github.com/cran/miloR
Date/Publication: 2023-10-24
Number of recursive dependencies: 197

Run revdep_details(, "miloR") for more info

checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: data 1.8Mb doc 5.4Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .fromMatrix: no visible binding for global variable ‘sce’ plotDAbeeswarm: no visible binding for global variable ‘SpatialFDR’ plotDAbeeswarm: no visible binding for global variable ‘logFC’ plotDAbeeswarm: no visible binding for global variable ‘is_signif’ plotDAbeeswarm: no visible binding for global variable ‘Nhood’ plotDAbeeswarm: no visible binding for global variable ‘logFC_color’ plotNhoodCounts: no visible binding for global variable ‘values’ plotNhoodCounts: no visible binding for global variable ‘..y..’ plotNhoodExpressionDA: no visible binding for global variable ‘Nhood’ plotNhoodExpressionDA: no visible binding for global variable ‘logFC’ ... plotNhoodMA: no visible binding for global variable ‘logFC’ plotNhoodMA: no visible binding for global variable ‘Sig’ plotNhoodSizeHist: no visible binding for global variable ‘nh_size’ Undefined global functions or variables: . ..y.. Nhood NhoodGroup Sig SpatialFDR avg_expr feature is_signif label layout logCPM logFC logFC_color logFC_rank nh_size sce size values weight Consider adding importFrom("graphics", "layout") to your NAMESPACE file.

MinimumDistance

Version: 1.46.0
GitHub: NA
Source code: https://github.com/cran/MinimumDistance
Date/Publication: 2023-10-24
Number of recursive dependencies: 84

Run revdep_details(, "MinimumDistance") for more info

checking whether package ‘MinimumDistance’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/MinimumDistance/new/MinimumDistance.Rcheck/00install.out’ for details.
checking Rd files ... WARNING checkRd: (5) MinimumDistance.Rd:0-7: Must have a \description
checking for code/documentation mismatches ... WARNING Functions or methods with usage in documentation object 'coerce' but not in code: ‘as’
checking Rd \usage sections ... WARNING ``` Objects in \usage without \alias in documentation object 'coerce': ‘as’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking contents of ‘data’ directory ... WARNING Output for data("trioSetListExample", package = "MinimumDistance"): Warning message: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doSNOW’
checking startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘MatrixGenerics’ All declared Imports should be used.
checking R code for possible problems ... NOTE callDenovoSegments: no visible global function definition for ‘read.bsfiles’ combineRanges: no visible global function definition for ‘RangedData’ getRefGene: no visible global function definition for ‘RangedData’ overlapsCentromere: no visible global function definition for ‘RangedData’ pruneMD: no visible global function definition for ‘RangedDataCBS’ pruneTrioSet: no visible global function definition for ‘RangedDataList’ read.bsfiles2: no visible binding for global variable ‘read.bsfiles’ GenomeAnnotatedDataFrameFrom,character: no visible global function definition for ‘read.bsfiles’ calculateMindist,list: no visible binding for global variable ‘elt’ Undefined global functions or variables: RangedData RangedDataCBS RangedDataList elt read.bsfiles

mixOmics

Version: 6.26.0
GitHub: https://github.com/mixOmicsTeam/mixOmics
Source code: https://github.com/cran/mixOmics
Date/Publication: 2023-10-24
Number of recursive dependencies: 98

Run revdep_details(, "mixOmics") for more info

checking installed package size ... NOTE installed size is 23.2Mb sub-directories of 1Mb or more: R 1.4Mb data 3.3Mb doc 17.1Mb

mnem

Version: 1.18.0
GitHub: https://github.com/cbg-ethz/mnem
Source code: https://github.com/cran/mnem
Date/Publication: 2023-10-24
Number of recursive dependencies: 181

Run revdep_details(, "mnem") for more info

checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: data 2.3Mb doc 3.8Mb libs 2.4Mb

moanin

Version: 1.10.0
GitHub: NA
Source code: https://github.com/cran/moanin
Date/Publication: 2023-10-24
Number of recursive dependencies: 128

Run revdep_details(, "moanin") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘documentation.Rmd’ using knitr

Quitting from lines 45-49 [unnamed-chunk-2] (documentation.Rmd) Error: processing vignette 'documentation.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘documentation.Rmd’

SUMMARY: processing the following file failed: ‘documentation.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘edge’ Unknown package ‘KEGGprofile’ in Rd xrefs

MOCHA

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/MOCHA
Date/Publication: 2023-06-12 12:30:07 UTC
Number of recursive dependencies: 231

Run revdep_details(, "MOCHA") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘ArchR’
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'purrr' All declared Imports should be used.

monocle

Version: 2.30.0
GitHub: NA
Source code: https://github.com/cran/monocle
Date/Publication: 2023-10-24
Number of recursive dependencies: 258

Run revdep_details(, "monocle") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘monocle-vignette.Rnw’ using knitr Error: processing vignette 'monocle-vignette.Rnw' failed with diagnostics: Running 'texi2dvi' on 'monocle-vignette.tex' failed. LaTeX errors: ! LaTeX Error: Filesectsty.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.37 \sectionfont {\sffamily\bfseries\color{RoyalBlue}\sectionrule{0pt}{0pt}{... ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘monocle-vignette.Rnw’

SUMMARY: processing the following file failed: ‘monocle-vignette.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rcpp’ ‘biocViews’ All declared Imports should be used.
checking R code for possible problems ... NOTE assign_cell_lineage: no visible global function definition for ‘nei’ buildBranchCellDataSet: no visible global function definition for ‘nei’ count_leaf_descendents: no visible global function definition for ‘nei’ cth_classifier_cds: no visible global function definition for ‘nei’ cth_classifier_cell: no visible global function definition for ‘nei’ diff_test_helper: no visible binding for global variable ‘Size_Factor’ exportCDS: no visible binding for global variable ‘use_for_ordering’ extract_good_ordering: no visible global function definition for ‘nei’ fit_model_helper: no visible binding for global variable ‘Size_Factor’ get_next_node_id: no visible binding for '<<-' assignment to ... variable ‘Branch’ project2MST: no visible global function definition for ‘nei’ reverseEmbeddingCDS : <anonymous>: no visible global function definition for ‘quantile’ Undefined global functions or variables: Branch Size_Factor nei next_node pseudocount quantile use_for_ordering Consider adding importFrom("stats", "quantile") to your NAMESPACE file.

MOSim

Version: 1.16.0
GitHub: https://github.com/ConesaLab/MOSim
Source code: https://github.com/cran/MOSim
Date/Publication: 2023-10-24
Number of recursive dependencies: 84

Run revdep_details(, "MOSim") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘MOSim.Rnw’ using knitr

Quitting from lines 245-271 [code6] (MOSim.Rnw) Error: processing vignette 'MOSim.Rnw' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘MOSim.Rnw’

SUMMARY: processing the following file failed: ‘MOSim.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: data 4.2Mb

motifbreakR

Version: 2.16.0
GitHub: https://github.com/Simon-Coetzee/motifbreakR
Source code: https://github.com/cran/motifbreakR
Date/Publication: 2023-10-24
Number of recursive dependencies: 180

Run revdep_details(, "motifbreakR") for more info

checking for missing documentation entries ... WARNING Undocumented data sets: 'example.pvalue' All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking dependencies in R code ... NOTE Package in Depends field not imported from: 'MotifDb' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking data for non-ASCII characters ... NOTE Note: found 6 marked UTF-8 strings

mrfDepth

Version: 1.0.15
GitHub: NA
Source code: https://github.com/cran/mrfDepth
Date/Publication: 2023-10-06 10:00:07 UTC
Number of recursive dependencies: 44

Run revdep_details(, "mrfDepth") for more info

checking installed package size ... NOTE installed size is 22.7Mb sub-directories of 1Mb or more: data 1.6Mb libs 20.8Mb

MultiBD

Version: 0.2.0
GitHub: NA
Source code: https://github.com/cran/MultiBD
Date/Publication: 2016-12-05 18:28:46
Number of recursive dependencies: 79

Run revdep_details(, "MultiBD") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: --- re-building ‘SIR-MCMC.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'SIR-MCMC.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/MultiBD/new/MultiBD.Rcheck/vign_test/MultiBD/vignettes/SIR-MCMC.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SIR-MCMC.log for more info. --- failed re-building ‘SIR-MCMC.Rmd’ ... l.75 \usepackage {amsmath}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘SIRtrans.Rnw’

SUMMARY: processing the following files failed: ‘SIR-MCMC.Rmd’ ‘SIRtrans.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 10.3Mb sub-directories of 1Mb or more: libs 8.8Mb

muscat

Version: 1.16.0
GitHub: https://github.com/HelenaLC/muscat
Source code: https://github.com/cran/muscat
Date/Publication: 2023-10-24
Number of recursive dependencies: 239

Run revdep_details(, "muscat") for more info

checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: doc 6.0Mb
checking R code for possible problems ... NOTE pbHeatmap: no visible binding for global variable ‘gene’ pbHeatmap: no visible binding for global variable ‘p_adj.loc’ pbHeatmap: no visible binding for global variable ‘logFC’ Undefined global functions or variables: gene logFC p_adj.loc

muscData

Version: 1.16.0
GitHub: https://github.com/HelenaLC/muscData
Source code: https://github.com/cran/muscData
Date/Publication: 2023-10-26
Number of recursive dependencies: 280

Run revdep_details(, "muscData") for more info

checking for missing documentation entries ... WARNING Undocumented code objects: ‘Crowell19_4vs4’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘SingleCellExperiment’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

NanoStringDiff

Version: 1.32.0
GitHub: NA
Source code: https://github.com/cran/NanoStringDiff
Date/Publication: 2023-10-24
Number of recursive dependencies: 59

Run revdep_details(, "NanoStringDiff") for more info

checking for missing documentation entries ... WARNING Undocumented code objects: ‘compute.baseSigma’ ‘est.dispersion’ ‘fun5’ ‘glmfit.OneGroup’ ‘glmfit.full’ ‘glmfit.reduce’ ‘rnegbinom’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking installed files from ‘inst/doc’ ... NOTE The following files look like leftovers/mistakes: ‘NanoStringDiff.log’ Please remove them from your package.
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘NanoStringDiff.Rnw’ using Sweave Loading required package: Biobase Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:
```
IQR, mad, sd, var, xtabs
```
... l.37 \sectionfont {\sffamily\bfseries\color{BiocBlue}\sectionrule{0pt}{0pt}{-... ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘NanoStringDiff.Rnw’

SUMMARY: processing the following file failed: ‘NanoStringDiff.Rnw’

Error: Vignette re-building failed. Execution halted ```

nearBynding

Version: 1.12.0
GitHub: NA
Source code: https://github.com/cran/nearBynding
Date/Publication: 2023-10-24
Number of recursive dependencies: 131

Run revdep_details(, "nearBynding") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘nearBynding.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'nearBynding.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/nearBynding/new/nearBynding.Rcheck/vign_test/nearBynding/vignettes/nearBynding.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See nearBynding.log for more info. --- failed re-building ‘nearBynding.Rmd’

SUMMARY: processing the following file failed: ‘nearBynding.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: extdata 6.9Mb

netZooR

Version: 1.6.0
GitHub: https://github.com/netZoo/netZooR
Source code: https://github.com/cran/netZooR
Date/Publication: 2023-10-24
Number of recursive dependencies: 229

Run revdep_details(, "netZooR") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: [1] 187 [1] 188 [1] 189 [1] 190 [1] 191 [1] 192 ... Backtrace: ▆
1. └─netZooR::pandaPy(...) at test-panda.R:29:3
2. └─reticulate::source_python(pandapath, convert = TRUE)
3. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
4. └─reticulate:::py_run_file_impl(file, local, convert)
[ FAIL 1 | WARN 1 | SKIP 1 | PASS 48 ] Error: Test failures Execution halted ```
checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 1.5Mb extdata 2.8Mb
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘matrixcalc’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE estimatePenaltyParameters: no visible global function definition for ‘matrix.trace’ runEgret: no visible binding for global variable ‘NA12878’ show,panda: no visible global function definition for ‘print.panda’ Undefined global functions or variables: NA12878 matrix.trace print.panda

NormalyzerDE

Version: 1.20.0
GitHub: https://github.com/ComputationalProteomics/NormalyzerDE
Source code: https://github.com/cran/NormalyzerDE
Date/Publication: 2023-10-24
Number of recursive dependencies: 127

Run revdep_details(, "NormalyzerDE") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

numbat

Version: 1.3.2-1
GitHub: https://github.com/kharchenkolab/numbat
Source code: https://github.com/cran/numbat
Date/Publication: 2023-06-17 18:50:02 UTC
Number of recursive dependencies: 136

Run revdep_details(, "numbat") for more info

checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: data 4.2Mb libs 4.8Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R.utils’ ‘optparse’ ‘vcfR’ All declared Imports should be used.
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

omicplotR

Version: 1.22.0
GitHub: NA
Source code: https://github.com/cran/omicplotR
Date/Publication: 2023-10-24
Number of recursive dependencies: 105

Run revdep_details(, "omicplotR") for more info

checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘ALDEx2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

omicsPrint

Version: 1.22.0
GitHub: NA
Source code: https://github.com/cran/omicsPrint
Date/Publication: 2023-10-24
Number of recursive dependencies: 142

Run revdep_details(, "omicsPrint") for more info

checking LazyData ... WARNING LazyData DB of 7.3 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions'
checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: data 7.3Mb doc 1.2Mb

omicsViewer

Version: 1.6.0
GitHub: https://github.com/mengchen18/omicsViewer
Source code: https://github.com/cran/omicsViewer
Date/Publication: 2023-10-24
Number of recursive dependencies: 191

Run revdep_details(, "omicsViewer") for more info

checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: extdata 4.8Mb

OncoBayes2

Version: 0.8-9
GitHub: NA
Source code: https://github.com/cran/OncoBayes2
Date/Publication: 2023-07-20 18:40:05 UTC
Number of recursive dependencies: 102

Run revdep_details(, "OncoBayes2") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘cmdstanr’
checking installed package size ... NOTE installed size is 72.7Mb sub-directories of 1Mb or more: libs 70.9Mb
checking startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_blrm_exnex” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_blrm_exnex” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

OptimalDesign

Version: 1.0.1
GitHub: NA
Source code: https://github.com/cran/OptimalDesign
Date/Publication: 2019-12-02 08:50:07 UTC
Number of recursive dependencies: 41

Run revdep_details(, "OptimalDesign") for more info

checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'gurobi', 'slam'
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

OUTRIDER

Version: 1.20.0
GitHub: https://github.com/gagneurlab/OUTRIDER
Source code: https://github.com/cran/OUTRIDER
Date/Publication: 2023-10-24
Number of recursive dependencies: 178

Run revdep_details(, "OUTRIDER") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘OUTRIDER.Rnw’ using knitr The magick package is required to crop "figure/deVsOutlier-1.png" but not available. The magick package is required to crop "figure/quick_guide-1.png" but not available. The magick package is required to crop "figure/filtering-1.png" but not available. The magick package is required to crop "figure/filtering-2.png" but not available. The magick package is required to crop "figure/plotting_between_sample_correlations-1.png" but not available. The magick package is required to crop "figure/plotting_between_sample_correlations-2.png" but not available. The magick package is required to crop "figure/controlling_for_confounders-1.png" but not available. The magick package is required to crop "figure/aberrantperSample-1.png" but not available. ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘OUTRIDER.Rnw’

SUMMARY: processing the following file failed: ‘OUTRIDER.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: doc 2.3Mb libs 3.1Mb
checking R code for possible problems ... NOTE padjOnSubset: no visible global function definition for ‘bpmapply’ Undefined global functions or variables: bpmapply

pandaR

Version: 1.34.0
GitHub: NA
Source code: https://github.com/cran/pandaR
Date/Publication: 2023-10-24
Number of recursive dependencies: 62

Run revdep_details(, "pandaR") for more info

checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
checking LazyData ... WARNING LazyData DB of 9.0 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions'
checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: data 9.0Mb
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'summary.panda': ‘summary.panda’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

pARI

Version: 1.1.1
GitHub: https://github.com/angeella/pARI
Source code: https://github.com/cran/pARI
Date/Publication: 2022-01-10 08:22:42 UTC
Number of recursive dependencies: 40

Run revdep_details(, "pARI") for more info

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: libs 5.1Mb

PathoStat

Version: 1.28.0
GitHub: https://github.com/mani2012/PathoStat
Source code: https://github.com/cran/PathoStat
Date/Publication: 2023-10-24
Number of recursive dependencies: 198

Run revdep_details(, "PathoStat") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ComplexHeatmap’ ‘RColorBrewer’ All declared Imports should be used.

pcaMethods

Version: 1.94.0
GitHub: https://github.com/hredestig/pcamethods
Source code: https://github.com/cran/pcaMethods
Date/Publication: 2023-10-24
Number of recursive dependencies: 32

Run revdep_details(, "pcaMethods") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ade4’

PDATK

Version: 1.10.0
GitHub: https://github.com/bhklab/PDATK
Source code: https://github.com/cran/PDATK
Date/Publication: 2023-10-24
Number of recursive dependencies: 269

Run revdep_details(, "PDATK") for more info

checking whether package ‘PDATK’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/PDATK/new/PDATK.Rcheck/00install.out’ for details.
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'rankFeatures-MultiAssayExperiment-method.Rd': ‘[dplyr:ranking]{dplyr::dense_rank}’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: doc 3.3Mb
checking R code for possible problems ... NOTE .calculateMSMthresholds: no visible binding for global variable ‘funContext’ .plotNetwork: no visible global function definition for ‘legend’ NCSModel: no visible binding for global variable ‘metric’ NCSModel: no visible binding for global variable ‘comparison’ NCSModel: no visible binding for global variable ‘centroid_K’ NCSModel: no visible binding for global variable ‘assay_K’ NetworkCommunitySearchModel: no visible binding for global variable ‘metric’ NetworkCommunitySearchModel: no visible binding for global variable ... trainModel,NCSModel: no visible binding for global variable ‘cor_threshold’ Undefined global functions or variables: .error assay_K assay_cohort centroid_K centroid_cohort cluster_label comparison cor_threshold dev.off feature feature_rank feature_score funContext ingroup_proportion legend metric missignAssays pdf tmp Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "legend") to your NAMESPACE file.

penppml

Version: 0.2.3
GitHub: https://github.com/tomzylkin/penppml
Source code: https://github.com/cran/penppml
Date/Publication: 2023-09-08 14:10:02 UTC
Number of recursive dependencies: 131

Run revdep_details(, "penppml") for more info

checking installed package size ... NOTE installed size is 11.5Mb sub-directories of 1Mb or more: data 1.8Mb libs 9.4Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘fixest’ All declared Imports should be used.

PepsNMR

Version: 1.20.0
GitHub: https://github.com/ManonMartin/PepsNMR
Source code: https://github.com/cran/PepsNMR
Date/Publication: 2023-10-24
Number of recursive dependencies: 66

Run revdep_details(, "PepsNMR") for more info

checking Rd files ... NOTE checkRd: (-1) Normalization.Rd:47: Escaped LaTeX specials: \&

phosphonormalizer

Version: 1.26.0
GitHub: NA
Source code: https://github.com/cran/phosphonormalizer
Date/Publication: 2023-10-24
Number of recursive dependencies: 55

Run revdep_details(, "phosphonormalizer") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘MSnbase’

Pigengene

Version: 1.28.0
GitHub: NA
Source code: https://github.com/cran/Pigengene
Date/Publication: 2023-10-24
Number of recursive dependencies: 204

Run revdep_details(, "Pigengene") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘Pigengene_inference.Rnw’ using knitr Error: processing vignette 'Pigengene_inference.Rnw' failed with diagnostics: Running 'texi2dvi' on 'Pigengene_inference.tex' failed. LaTeX errors: ! LaTeX Error: Filenowidow.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty) ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘Pigengene_inference.Rnw’

SUMMARY: processing the following file failed: ‘Pigengene_inference.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ``` Found the following possibly unsafe calls: File ‘Pigengene/R/bn.calculation.R’: assignInNamespace("supported.clusters", fixArgs, "bnlearn")

one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db ```

PINSPlus

Version: 2.0.6
GitHub: NA
Source code: https://github.com/cran/PINSPlus
Date/Publication: 2021-12-14 19:40:02 UTC
Number of recursive dependencies: 50

Run revdep_details(, "PINSPlus") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

pipeComp

Version: 1.12.0
GitHub: https://github.com/plger/pipeComp
Source code: https://github.com/cran/pipeComp
Date/Publication: 2023-10-24
Number of recursive dependencies: 211

Run revdep_details(, "pipeComp") for more info

checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: doc 4.5Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.compileExcludedCells’ ‘.getMM’ ‘.homogenizeDEA’ ‘.runf’
checking R code for possible problems ... NOTE scrna_describeDatasets: no visible binding for global variable ‘cluster’ scrna_describeDatasets: no visible binding for global variable ‘nb’ scrna_describeDatasets : pf: no visible binding for global variable ‘.x’ scrna_describeDatasets : rd: no visible binding for global variable ‘y’ scrna_describeDatasets : rd: no visible binding for global variable ‘cluster’ scrna_evalPlot_filtering: no visible binding for global variable ‘max.lost’ ... scrna_evalPlot_filtering: no visible binding for global variable ‘doubletmethod’ scrna_evalPlot_filtering: no visible binding for global variable ‘method’ scrna_evalPlot_overall: no visible binding for global variable ‘true.nbClusts’ scrna_evalPlot_overall: no visible binding for global variable ‘n_clus’ Undefined global functions or variables: .x cluster doubletmethod filt max.lost mean_F1 method n_clus nb true.nbClusts y
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘edgeR’ ‘sva’

pmp

Version: 1.14.0
GitHub: NA
Source code: https://github.com/cran/pmp
Date/Publication: 2023-10-24
Number of recursive dependencies: 111

Run revdep_details(, "pmp") for more info

checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: data 1.8Mb doc 5.7Mb

ProteoDisco

Version: 1.8.0
GitHub: https://github.com/ErasmusMC-CCBC/ProteoDisco
Source code: https://github.com/cran/ProteoDisco
Date/Publication: 2023-10-24
Number of recursive dependencies: 190

Run revdep_details(, "ProteoDisco") for more info

checking whether package ‘ProteoDisco’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘dplyr::rename’ by ‘plyr::rename’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::count’ by ‘plyr::count’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::failwith’ by ‘plyr::failwith’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::id’ by ‘plyr::id’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarize’ by ‘plyr::summarize’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::summarise’ by ‘plyr::summarise’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::mutate’ by ‘plyr::mutate’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::desc’ by ‘plyr::desc’ when loading ‘ProteoDisco’ Warning: replacing previous import ‘dplyr::arrange’ by ‘plyr::arrange’ when loading ‘ProteoDisco’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/ProteoDisco/new/ProteoDisco.Rcheck/00install.out’ for details.
checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'show' and siglist 'ProteoDiscography' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘ProteoDisco’ for: ‘show’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking data for non-ASCII characters ... NOTE ``` Error loading dataset 'ProteoDiscographyExample.hg19': Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'seqlevels': UCSC library operation failed

```

ProteoMM

Version: 1.20.0
GitHub: NA
Source code: https://github.com/cran/ProteoMM
Date/Publication: 2023-10-24
Number of recursive dependencies: 101

Run revdep_details(, "ProteoMM") for more info

checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT

QDNAseq

Version: 1.38.0
GitHub: https://github.com/ccagc/QDNAseq
Source code: https://github.com/cran/QDNAseq
Date/Publication: 2023-10-24
Number of recursive dependencies: 93

Run revdep_details(, "QDNAseq") for more info

R CMD check timed out

Qest

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/Qest
Date/Publication: 2022-04-05 09:20:02 UTC
Number of recursive dependencies: 69

Run revdep_details(, "Qest") for more info

checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'internals': ‘format.perc’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

QFeatures

Version: 1.12.0
GitHub: https://github.com/RforMassSpectrometry/QFeatures
Source code: https://github.com/cran/QFeatures
Date/Publication: 2023-10-25
Number of recursive dependencies: 158

Run revdep_details(, "QFeatures") for more info

checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'QFeatures-aggregate.Rd': ‘sparseMatrix’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: doc 4.3Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘MultiAssayExperiment:::.sampleMapFromData’ See the note in ?`:::` about the use of this operator.

RaceID

Version: 0.3.3
GitHub: NA
Source code: https://github.com/cran/RaceID
Date/Publication: 2023-09-28 10:10:08 UTC
Number of recursive dependencies: 144

Run revdep_details(, "RaceID") for more info

checking installed package size ... NOTE installed size is 11.8Mb sub-directories of 1Mb or more: data 2.1Mb doc 6.7Mb libs 2.2Mb

rADA

Version: 1.1.9
GitHub: NA
Source code: https://github.com/cran/rADA
Date/Publication: 2021-03-23 19:40:06 UTC
Number of recursive dependencies: 115

Run revdep_details(, "rADA") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘rada_vignette.Rmd’ using knitr

Quitting from lines 62-70 [unnamed-chunk-2] (rada_vignette.Rmd) Error: processing vignette 'rada_vignette.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘rada_vignette.Rmd’

--- re-building ‘rada_vignette_supplemental.Rmd’ using knitr ... Quitting from lines 62-70 [unnamed-chunk-2] (rada_vignette_supplemental.Rmd) Error: processing vignette 'rada_vignette_supplemental.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘rada_vignette_supplemental.Rmd’

SUMMARY: processing the following files failed: ‘rada_vignette.Rmd’ ‘rada_vignette_supplemental.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: doc 5.5Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’ All declared Imports should be used.

RadioGx

Version: 2.6.0
GitHub: NA
Source code: https://github.com/cran/RadioGx
Date/Publication: 2023-10-24
Number of recursive dependencies: 145

Run revdep_details(, "RadioGx") for more info

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: data 3.5Mb
checking data for non-ASCII characters ... NOTE Note: found 52 marked UTF-8 strings

RandomForestsGLS

Version: 0.1.4
GitHub: https://github.com/ArkajyotiSaha/RandomForestsGLS
Source code: https://github.com/cran/RandomForestsGLS
Date/Publication: 2022-04-28 13:30:08 UTC
Number of recursive dependencies: 75

Run revdep_details(, "RandomForestsGLS") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘RandomForestsGLS_user_guide.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'RandomForestsGLS_user_guide.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/RandomForestsGLS/new/RandomForestsGLS.Rcheck/vign_test/RandomForestsGLS/vignettes/RandomForestsGLS_user_guide.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RandomForestsGLS_user_guide.log for more info. --- failed re-building ‘RandomForestsGLS_user_guide.Rmd’

SUMMARY: processing the following file failed: ‘RandomForestsGLS_user_guide.Rmd’

Error: Vignette re-building failed. Execution halted ```

RBesT

Version: 1.7-2
GitHub: https://github.com/Novartis/RBesT
Source code: https://github.com/cran/RBesT
Date/Publication: 2023-08-22 00:00:02 UTC
Number of recursive dependencies: 144

Run revdep_details(, "RBesT") for more info

checking installed package size ... NOTE installed size is 96.0Mb sub-directories of 1Mb or more: doc 1.1Mb libs 93.5Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

regsem

Version: 1.9.5
GitHub: https://github.com/Rjacobucci/regsem
Source code: https://github.com/cran/regsem
Date/Publication: 2023-06-02 09:00:02 UTC
Number of recursive dependencies: 177

Run revdep_details(, "regsem") for more info

checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: libs 6.0Mb

reservr

Version: 0.0.2
GitHub: https://github.com/AshesITR/reservr
Source code: https://github.com/cran/reservr
Date/Publication: 2023-10-18 20:50:05 UTC
Number of recursive dependencies: 144

Run revdep_details(, "reservr") for more info

checking installed package size ... NOTE installed size is 16.8Mb sub-directories of 1Mb or more: R 1.5Mb libs 14.7Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

RGCCA

Version: 3.0.2
GitHub: https://github.com/rgcca-factory/RGCCA
Source code: https://github.com/cran/RGCCA
Date/Publication: 2023-10-09 15:40:02 UTC
Number of recursive dependencies: 187

Run revdep_details(, "RGCCA") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘RGCCA.Rmd’ using rmarkdown ! Package pgfkeys Error: I do not know the key '/tikz/orcidlogo/.pic' and I am going to ignore it. Perhaps you misspelled it.

Error: processing vignette 'RGCCA.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/RGCCA/new/RGCCA.Rcheck/vign_test/RGCCA/vignettes/RGCCA.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RGCCA.log for more info. --- failed re-building ‘RGCCA.Rmd’

SUMMARY: processing the following file failed: ‘RGCCA.Rmd’

Error: Vignette re-building failed. Execution halted ```

RiboDiPA

Version: 1.10.0
GitHub: NA
Source code: https://github.com/cran/RiboDiPA
Date/Publication: 2023-10-24
Number of recursive dependencies: 148

Run revdep_details(, "RiboDiPA") for more info

checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: data 2.9Mb doc 1.3Mb libs 1.3Mb

RJcluster

Version: 3.2.4
GitHub: NA
Source code: https://github.com/cran/RJcluster
Date/Publication: 2022-02-14 21:30:02 UTC
Number of recursive dependencies: 63

Run revdep_details(, "RJcluster") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘RJclust_Vignette.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'RJclust_Vignette.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/RJcluster/new/RJcluster.Rcheck/vign_test/RJcluster/vignettes/RJclust_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RJclust_Vignette.log for more info. --- failed re-building ‘RJclust_Vignette.Rmd’

SUMMARY: processing the following file failed: ‘RJclust_Vignette.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: libs 6.9Mb

RNAmodR

Version: 1.16.0
GitHub: https://github.com/FelixErnst/RNAmodR
Source code: https://github.com/cran/RNAmodR
Date/Publication: 2023-10-24
Number of recursive dependencies: 196

Run revdep_details(, "RNAmodR") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/1491ca97848_2537' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/1491cd7cffc0_2549' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/1491c74f971cc_2539' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/1491c729e5372_2541' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/1477b1b7a8295_2543' [E::idx_find_and_load] Could not retrieve index file for '/c4/home/henrik/.cache/R/ExperimentHub/1491c206ed2db_2545' ...
1. ├─testthat::expect_error(...) at test-2Modifier.R:137:2
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─RNAmodR:::.get_classname_for_ModifierSet_from_modifier_type("DataFrame")
[ FAIL 1 | WARN 27 | SKIP 0 | PASS 898 ] Error: Test failures Execution halted ```
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'Biostrings:::XString' 'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList' 'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine' 'S4Vectors:::make_zero_col_DataFrame' 'S4Vectors:::prepare_objects_to_bind' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.get_inosine_score'

RNAseqQC

Version: 0.1.4
GitHub: NA
Source code: https://github.com/cran/RNAseqQC
Date/Publication: 2022-06-15 09:50:06 UTC
Number of recursive dependencies: 177

Run revdep_details(, "RNAseqQC") for more info

checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 3.5Mb doc 2.2Mb

RnBeads

Version: 2.20.0
GitHub: NA
Source code: https://github.com/cran/RnBeads
Date/Publication: 2023-10-24
Number of recursive dependencies: 267

Run revdep_details(, "RnBeads") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster', 'ff', 'fields', 'ggplot2', 'gplots', 'grid', 'gridExtra', 'limma', 'matrixStats', 'illuminaio', 'methylumi', 'plyr' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: R 3.1Mb doc 3.7Mb
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘qvalue’ A package should be listed in only one of these fields.
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking dependencies in R code ... NOTE Package in Depends field not imported from: 'grid' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: 'Gviz:::.getBMFeatureMap' 'doParallel:::.options' 'grDevices:::.smoothScatterCalcDensity' 'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k' 'minfi:::.normalizeFunnorm450k' See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .stopImplicitCluster: no visible global function definition for ‘stopCluster’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘phenoData’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘assayDataElementNames’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘featureNames’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘varLabels’ ... plotTracks preprocessSWAN pvalues qvalue readMethylome readSNPTable refText reg.type region.size registerDoParallel relative.coord removeSNPs report runLOLA samples segmentPMDs segmentUMRsLMRs seqlengths seqlevels<- setNames sigCategories sigset.l sites2ignore size solve.QP stopCluster sva target texthere tsne type types ucscTableQuery universeCounts useMart v var.diff varFit varLabels x x2 xmlValue y y2 yint Consider adding importFrom("stats", "setNames") to your NAMESPACE file.
checking re-building of vignette outputs ... NOTE `` Error(s) in re-building vignettes: --- re-building ‘RnBeads.Rnw’ using Sweave Error: processing vignette 'RnBeads.Rnw' failed with diagnostics: Running 'texi2dvi' on 'RnBeads.tex' failed. LaTeX errors: ! LaTeX Error: Filevmargin.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

... l.10 \usepackage [english,american]{babel}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘RnBeads_Annotations.Rnw’

SUMMARY: processing the following files failed: ‘RnBeads.Rnw’ ‘RnBeads_Annotations.Rnw’

Error: Vignette re-building failed. Execution halted ```

robustlm

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/robustlm
Date/Publication: 2021-03-22 15:40:02 UTC
Number of recursive dependencies: 33

Run revdep_details(, "robustlm") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

rpm

Version: 0.7-1
GitHub: https://github.com/handcock/rpm
Source code: https://github.com/cran/rpm
Date/Publication: 2023-04-21 23:30:02 UTC
Number of recursive dependencies: 68

Run revdep_details(, "rpm") for more info

checking installed package size ... NOTE installed size is 11.6Mb sub-directories of 1Mb or more: libs 11.1Mb

rsvddpd

Version: 1.0.0
GitHub: https://github.com/subroy13/rsvddpd
Source code: https://github.com/cran/rsvddpd
Date/Publication: 2021-10-27 14:30:02 UTC
Number of recursive dependencies: 39

Run revdep_details(, "rsvddpd") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

rtrend

Version: 0.1.4
GitHub: https://github.com/rpkgs/rtrend
Source code: https://github.com/cran/rtrend
Date/Publication: 2022-11-07 08:20:02 UTC
Number of recursive dependencies: 71

Run revdep_details(, "rtrend") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector2” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVector2” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```

samr

Version: 3.0
GitHub: NA
Source code: https://github.com/cran/samr
Date/Publication: 2018-10-16 10:00:03 UTC
Number of recursive dependencies: 44

Run revdep_details(, "samr") for more info

checking Rd files ... NOTE checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$ checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$ checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$ checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$ checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$ checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \# checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#

SANvi

Version: 0.1.0
GitHub: https://github.com/fradenti/SANvi
Source code: https://github.com/cran/SANvi
Date/Publication: 2023-10-10 17:20:05 UTC
Number of recursive dependencies: 15

Run revdep_details(, "SANvi") for more info

checking installed package size ... NOTE installed size is 9.6Mb sub-directories of 1Mb or more: libs 9.1Mb

scDataviz

Version: 1.12.0
GitHub: https://github.com/kevinblighe/scDataviz
Source code: https://github.com/cran/scDataviz
Date/Publication: 2023-10-24
Number of recursive dependencies: 191

Run revdep_details(, "scDataviz") for more info

checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: doc 5.7Mb

scDHA

Version: 1.2.1
GitHub: https://github.com/duct317/scDHA
Source code: https://github.com/cran/scDHA
Date/Publication: 2023-04-04 12:10:02 UTC
Number of recursive dependencies: 64

Run revdep_details(, "scDHA") for more info

checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: data 3.2Mb libs 4.3Mb

scISR

Version: 0.1.1
GitHub: https://github.com/duct317/scISR
Source code: https://github.com/cran/scISR
Date/Publication: 2022-06-30 06:20:08 UTC
Number of recursive dependencies: 56

Run revdep_details(, "scISR") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘markdown’ All declared Imports should be used.

scmap

Version: 1.24.0
GitHub: https://github.com/hemberg-lab/scmap
Source code: https://github.com/cran/scmap
Date/Publication: 2023-10-24
Number of recursive dependencies: 87

Run revdep_details(, "scmap") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘scmap.Rmd’ using rmarkdown

Quitting from lines 15-17 [knitr-options] (scmap.Rmd) Error: processing vignette 'scmap.Rmd' failed with diagnostics: there is no package called 'codetools' --- failed re-building ‘scmap.Rmd’

SUMMARY: processing the following file failed: ‘scmap.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: data 2.6Mb doc 1.1Mb libs 2.3Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Biobase’ All declared Imports should be used.

scMET

Version: 1.4.0
GitHub: https://github.com/andreaskapou/scMET
Source code: https://github.com/cran/scMET
Date/Publication: 2023-10-24
Number of recursive dependencies: 112

Run revdep_details(, "scMET") for more info

checking installed package size ... NOTE installed size is 57.2Mb sub-directories of 1Mb or more: doc 3.4Mb libs 52.5Mb
checking startup messages can be suppressed ... NOTE ``` code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_scmet” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_rstantools_model_scmet” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

scone

Version: 1.26.0
GitHub: https://github.com/YosefLab/scone
Source code: https://github.com/cran/scone
Date/Publication: 2023-10-24
Number of recursive dependencies: 264

Run revdep_details(, "scone") for more info

checking R code for possible problems ... NOTE sconeReport: no visible global function definition for ‘visNetworkOutput’ sconeReport: no visible global function definition for ‘plotlyOutput’ sconeReport : server: no visible global function definition for ‘renderVisNetwork’ sconeReport : server: no visible global function definition for ‘%>%’ sconeReport : server: no visible global function definition for ‘visNetwork’ sconeReport : server: no visible global function definition for ‘visHierarchicalLayout’ ... sconeReport : server: no visible global function definition for ‘geom_point’ sconeReport : server: no visible global function definition for ‘guides’ Undefined global functions or variables: %>% aes coord_cartesian element_blank geom_bar geom_point geom_violin ggplot ggplotly guides labs plot_ly plotlyOutput renderVisNetwork scale_fill_manual theme visEdges visGroups visHierarchicalLayout visLegend visNetwork visNetworkOutput visNetworkProxy visOptions visSelectNodes ylim

scp

Version: 1.12.0
GitHub: https://github.com/UCLouvain-CBIO/scp
Source code: https://github.com/cran/scp
Date/Publication: 2023-10-24
Number of recursive dependencies: 196

Run revdep_details(, "scp") for more info

checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: doc 7.0Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘MultiAssayExperiment:::.sampleMapFromData’ ‘QFeatures:::.get_Hits’ ‘QFeatures:::.normIndex’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE readSCPfromDIANN: no visible global function definition for ‘pivot_wider’ Undefined global functions or variables: pivot_wider

scPCA

Version: 1.16.0
GitHub: https://github.com/PhilBoileau/scPCA
Source code: https://github.com/cran/scPCA
Date/Publication: 2023-10-24
Number of recursive dependencies: 168

Run revdep_details(, "scPCA") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DelayedArray’ ‘matrixStats’ All declared Imports should be used.

sctransform

Version: 0.4.1
GitHub: https://github.com/satijalab/sctransform
Source code: https://github.com/cran/sctransform
Date/Publication: 2023-10-19 04:40:02 UTC
Number of recursive dependencies: 70

Run revdep_details(, "sctransform") for more info

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘glmGamPoi’

seagull

Version: 1.1.0
GitHub: https://github.com/jklosa/seagull
Source code: https://github.com/cran/seagull
Date/Publication: 2021-04-20 12:10:02 UTC
Number of recursive dependencies: 55

Run revdep_details(, "seagull") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘seagull.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'seagull.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/seagull/new/seagull.Rcheck/vign_test/seagull/vignettes/seagull.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See seagull.log for more info. --- failed re-building ‘seagull.Rmd’

SUMMARY: processing the following file failed: ‘seagull.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 12.1Mb sub-directories of 1Mb or more: libs 11.5Mb

sechm

Version: 1.10.0
GitHub: https://github.com/plger/sechm
Source code: https://github.com/cran/sechm
Date/Publication: 2023-10-24
Number of recursive dependencies: 91

Run revdep_details(, "sechm") for more info

checking R code for possible problems ... NOTE homogenizeDEA: no visible global function definition for ‘head’ homogenizeDEA: no visible global function definition for ‘p.adjust’ setRowAttr : <anonymous>: no visible global function definition for ‘setNames’ Undefined global functions or variables: head p.adjust setNames Consider adding importFrom("stats", "p.adjust", "setNames") importFrom("utils", "head") to your NAMESPACE file.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ggplot2’

seqArchR

Version: 1.6.0
GitHub: https://github.com/snikumbh/seqArchR
Source code: https://github.com/cran/seqArchR
Date/Publication: 2023-10-24
Number of recursive dependencies: 124

Run revdep_details(, "seqArchR") for more info

checking examples ... ERROR ``` Running examples in ‘seqArchR-Ex.R’ failed The error most likely occurred in:

Name: seqArchR

Title: seqArchR: A package for de novo discovery of different sequence

architectures

Aliases: seqArchR

** Examples

...

── Outer chunk 1 of 1 [Size: 200] ──

── Inner chunk 1 of 2 [Size: 100] Error: BiocParallel errors 2 remote errors, element index: 1, 51 98 unevaluated and other errors first remote error: Error: Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 4. └─seqArchR (local) FUN(X[[i]], ...) 5. └─seqArchR:::.handle_chunk_w_NMF2(...) 6. └─seqArchR:::.stability_model_select_pyNMF2(...) 7. └─seqArchR:::.perform_multiple_NMF_runs(...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...) ... 5. └─seqArchR:::.handle_chunk_w_NMF2(...) 6. └─seqArchR:::.stability_model_select_pyNMF2(...) 7. └─seqArchR:::.perform_multiple_NMF_runs(...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...)
1. └─BiocParallel:::.bpinit(...)
[ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ] Error: Test failures Execution halted ```

Seurat

Version: 4.4.0
GitHub: https://github.com/satijalab/seurat
Source code: https://github.com/cran/Seurat
Date/Publication: 2023-09-28 08:50:05 UTC
Number of recursive dependencies: 259

Run revdep_details(, "Seurat") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: > library(Seurat) Attaching SeuratObject 'SeuratObject' was built under R 4.3.1 but the current version is 4.3.2; it is recomended that you reinstall 'SeuratObject' as the ABI for R may have changed Seurat v4 was just loaded with SeuratObject v5; disabling v5 assays and ...

══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_objects.R:46:3'): AddMetaData errors ───────────────────────── AddMetaData(...) did not throw an error. ── Failure ('test_preprocessing.R:43:3'): Metadata check errors correctly ────── CreateSeuratObject(counts = pbmc.test, meta.data = pbmc.md.norownames) did not throw an error.

[ FAIL 2 | WARN 5 | SKIP 19 | PASS 648 ] Error: Test failures Execution halted ```
checking S3 generic/method consistency ... WARNING HVFInfo: function(object, method, status, ...) HVFInfo.SCTAssay: function(object, selection.method, status, ...) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 14.7Mb sub-directories of 1Mb or more: R 1.4Mb libs 12.6Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Signac’

SGP

Version: 2.1-0.0
GitHub: https://github.com/CenterForAssessment/SGP
Source code: https://github.com/cran/SGP
Date/Publication: 2023-10-23 15:50:19 UTC
Number of recursive dependencies: 114

Run revdep_details(, "SGP") for more info

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: R 1.3Mb doc 3.8Mb

SIAMCAT

Version: 2.6.0
GitHub: NA
Source code: https://github.com/cran/SIAMCAT
Date/Publication: 2023-10-24
Number of recursive dependencies: 201

Run revdep_details(, "SIAMCAT") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 23.4Mb sub-directories of 1Mb or more: doc 18.4Mb extdata 2.1Mb help 1.9Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ranger’

SICtools

Version: 1.32.0
GitHub: NA
Source code: https://github.com/cran/SICtools
Date/Publication: 2023-10-24
Number of recursive dependencies: 43

Run revdep_details(, "SICtools") for more info

checking whether package ‘SICtools’ can be installed ... WARNING Found the following significant warnings: bam.c:128:2: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] bam_index.c:178:35: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] razf.c:178:2: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] md5.c:155:26: warning: argument to ‘sizeof’ in ‘memset’ call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’ See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/SICtools/new/SICtools.Rcheck/00install.out’ for details.
checking examples ... WARNING ``` Found the following significant warnings:

Warning: 'applyPileups' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'Rsamtools', 'doParallel', 'Biostrings', 'stringr', 'matrixStats', 'plyr', 'GenomicRanges', 'IRanges' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE .indelDiffFunc: no visible global function definition for ‘fisher.test’ .indelDiffFunc: no visible global function definition for ‘dist’ indelDiff: no visible global function definition for ‘read.delim’ snpDiff : calcInfoRange : <anonymous>: no visible global function definition for ‘fisher.test’ snpDiff : calcInfoRange : <anonymous>: no visible global function definition for ‘dist’ Undefined global functions or variables: dist fisher.test read.delim Consider adding importFrom("stats", "dist", "fisher.test") importFrom("utils", "read.delim") to your NAMESPACE file.

sigminer

Version: 2.2.2
GitHub: https://github.com/ShixiangWang/sigminer
Source code: https://github.com/cran/sigminer
Date/Publication: 2023-08-21 04:30:02 UTC
Number of recursive dependencies: 205

Run revdep_details(, "sigminer") for more info

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: extdata 1.6Mb help 1.7Mb libs 1.4Mb

signifinder

Version: 1.4.0
GitHub: https://github.com/CaluraLab/signifinder
Source code: https://github.com/cran/signifinder
Date/Publication: 2023-10-24
Number of recursive dependencies: 272

Run revdep_details(, "signifinder") for more info

checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: data 1.4Mb doc 5.1Mb
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘curatedTCGAData’, ‘EDASeq’

SimBu

Version: 1.4.0
GitHub: https://github.com/omnideconv/SimBu
Source code: https://github.com/cran/SimBu
Date/Publication: 2023-10-24
Number of recursive dependencies: 198

Run revdep_details(, "SimBu") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions .pre-commit-config.yaml .prettierignore These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking whether package ‘SimBu’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/SimBu/new/SimBu.Rcheck/00install.out’ for details.

simona

Version: 1.0.0
GitHub: https://github.com/jokergoo/simona
Source code: https://github.com/cran/simona
Date/Publication: 2023-10-24
Number of recursive dependencies: 138

Run revdep_details(, "simona") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 19.1Mb sub-directories of 1Mb or more: doc 5.7Mb libs 11.8Mb

simPop

Version: 2.1.2
GitHub: https://github.com/statistikat/simPop
Source code: https://github.com/cran/simPop
Date/Publication: 2022-11-07 15:10:02 UTC
Number of recursive dependencies: 132

Run revdep_details(, "simPop") for more info

checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: data 2.0Mb libs 5.0Mb

sindyr

Version: 0.2.3
GitHub: NA
Source code: https://github.com/cran/sindyr
Date/Publication: 2020-06-09 05:20:03 UTC
Number of recursive dependencies: 28

Run revdep_details(, "sindyr") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘crqa’ ‘plot3D’ All declared Imports should be used.

Single.mTEC.Transcriptomes

Version: 1.30.0
GitHub: NA
Source code: https://github.com/cran/Single.mTEC.Transcriptomes
Date/Publication: 2023-10-26
Number of recursive dependencies: 174

Run revdep_details(, "Single.mTEC.Transcriptomes") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘mTECs.Rnw’ using knitr The magick package is required to crop "figure/Figure_1C_variableNoMarker-1.png" but not available. The magick package is required to crop "figure/Figure_1A_trasvsgenes-1.png" but not available. The magick package is required to crop "figure/Figure_Supp1_percentageTRAs-1.png" but not available. The magick package is required to crop "figure/Figure_1B_saturation-1.png" but not available. The magick package is required to crop "figure/Figure_Supp2_traenrichment-1.png" but not available. The magick package is required to crop "figure/Figure_1D1_histogramAire-1.png" but not available. The magick package is required to crop "figure/Figure_1D2_histogramAire-1.png" but not available. The magick package is required to crop "figure/Figure_1D3_histogramAire-1.png" but not available. ... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘mTECs.Rnw’

SUMMARY: processing the following file failed: ‘mTECs.Rnw’

Error: Vignette re-building failed. Execution halted ```
checking installed package size ... NOTE installed size is 904.4Mb sub-directories of 1Mb or more: data 895.1Mb doc 9.3Mb

singleCellTK

Version: 2.12.0
GitHub: https://github.com/compbiomed/singleCellTK
Source code: https://github.com/cran/singleCellTK
Date/Publication: 2023-10-24
Number of recursive dependencies: 398

Run revdep_details(, "singleCellTK") for more info

checking tests ... ``` Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: ********|
```
|                                                                            
|                                                                      |   0%
|
```
... Backtrace: ▆ 1. └─singleCellTK::plotSeuratReduction(sce, useReduction = "pca") at test-seuratFunctions.R:41:2 2. └─Seurat::DimPlot(...) 3. ├─methods (local) [[<-(*tmp*, "ident", value = <fct>) 4. └─SeuratObject (local) [[<-(*tmp*, "ident", value = <fct>)

[ FAIL 1 | WARN 39 | SKIP 0 | PASS 209 ] Error: Test failures Execution halted ```
checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: extdata 1.5Mb shiny 2.7Mb

singscore

Version: 1.22.0
GitHub: https://github.com/DavisLaboratory/singscore
Source code: https://github.com/cran/singscore
Date/Publication: 2023-10-24
Number of recursive dependencies: 148

Run revdep_details(, "singscore") for more info

checking R code for possible problems ... NOTE plotDispersion: no visible binding for global variable ‘Score’ plotDispersion: no visible binding for global variable ‘Dispersion’ plotDispersion: no visible binding for global variable ‘Class’ plotDispersion: no visible binding for global variable ‘SampleText’ plotDispersion: no visible binding for global variable ‘SampleLabel’ plotRankDensity_intl: no visible binding for global variable ‘Ranks’ plotRankDensity_intl: no visible binding for global variable ‘upDown’ plotRankDensity_intl: no visible binding for global variable ‘..density..’ plotRankDensity_intl: no visible binding for global variable ‘EntrezID’ ... plotScoreLandscape: no visible binding for global variable ‘sc1’ plotScoreLandscape: no visible binding for global variable ‘sc2’ projectScoreLandscape: no visible binding for global variable ‘SampleText’ projectScoreLandscape: no visible binding for global variable ‘Class’ projectScoreLandscape: no visible binding for global variable ‘SampleLabel’ Undefined global functions or variables: ..density.. Class Dispersion EntrezID Ranks SampleLabel SampleText Score sc1 sc2 upDown

SkeweDF

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/SkeweDF
Date/Publication: 2021-01-16 09:40:05 UTC
Number of recursive dependencies: 28

Run revdep_details(, "SkeweDF") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

slasso

Version: 1.0.0
GitHub: https://github.com/unina-sfere/slasso
Source code: https://github.com/cran/slasso
Date/Publication: 2021-10-15 07:40:02 UTC
Number of recursive dependencies: 101

Run revdep_details(, "slasso") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘RcppArmadillo’ All declared Imports should be used.

sparrow

Version: 1.8.0
GitHub: https://github.com/lianos/sparrow
Source code: https://github.com/cran/sparrow
Date/Publication: 2023-10-24
Number of recursive dependencies: 207

Run revdep_details(, "sparrow") for more info

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: R 1.1Mb doc 2.0Mb extdata 2.1Mb
checking R code for possible problems ... NOTE geneSetsStats: no visible binding for global variable ‘direction’ Undefined global functions or variables: direction

SparseArray

Version: 1.2.0
GitHub: https://github.com/Bioconductor/SparseArray
Source code: https://github.com/cran/SparseArray
Date/Publication: 2023-10-24
Number of recursive dependencies: 67

Run revdep_details(, "SparseArray") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output:

The following objects are masked from 'package:Matrix':
```
  expand, unname
```
The following object is masked from 'package:utils': ... 1/9 mismatches [7] NaN - Inf == NaN Backtrace: ▆ 1. └─SparseArray (local) .test_sym_crossprod_SparseMatrix(m0, svt0) at test-SparseMatrix-mult.R:56:4 2. └─testthat (local) EXPECT_FUN(cp, crossprod(m, svt)) at test-SparseMatrix-mult.R:37:4

[ FAIL 2 | WARN 1 | SKIP 0 | PASS 5796 ] Error: Test failures Execution halted ```
checking compiled code ... NOTE ``` File ‘SparseArray/libs/SparseArray.so’: Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

sparseMatrixStats

Version: 1.14.0
GitHub: https://github.com/const-ae/sparseMatrixStats
Source code: https://github.com/cran/sparseMatrixStats
Date/Publication: 2023-10-24
Number of recursive dependencies: 62

Run revdep_details(, "sparseMatrixStats") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: libs 4.9Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘SummarizedExperiment’

spathial

Version: 0.1.2
GitHub: NA
Source code: https://github.com/cran/spathial
Date/Publication: 2020-04-10 18:20:02 UTC
Number of recursive dependencies: 43

Run revdep_details(, "spathial") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘irlba’ ‘knitr’ ‘rmarkdown’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

spatzie

Version: 1.8.0
GitHub: NA
Source code: https://github.com/cran/spatzie
Date/Publication: 2023-10-24
Number of recursive dependencies: 191

Run revdep_details(, "spatzie") for more info

checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.

splatter

Version: 1.26.0
GitHub: https://github.com/Oshlack/splatter
Source code: https://github.com/cran/splatter
Date/Publication: 2023-10-24
Number of recursive dependencies: 255

Run revdep_details(, "splatter") for more info

checking installed package size ... NOTE installed size is 10.0Mb sub-directories of 1Mb or more: doc 9.1Mb

SpliceWiz

Version: 1.4.0
GitHub: https://github.com/alexchwong/SpliceWiz
Source code: https://github.com/cran/SpliceWiz
Date/Publication: 2023-10-24
Number of recursive dependencies: 207

Run revdep_details(, "SpliceWiz") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 18.5Mb sub-directories of 1Mb or more: R 2.2Mb doc 4.9Mb libs 10.3Mb

SPOTlight

Version: 1.6.0
GitHub: https://github.com/MarcElosua/SPOTlight
Source code: https://github.com/cran/SPOTlight
Date/Publication: 2023-10-24
Number of recursive dependencies: 256

Run revdep_details(, "SPOTlight") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: 9. │ ├─methods::initialize(value, ...)
1. │ └─methods::initialize(value, ...)
2. └─SeuratObject::LogMap(y = cells.all)
3. └─methods::new(...)
4. ├─methods::initialize(value, ...)
5. └─methods::initialize(value, ...) ...
6. └─SeuratObject::LogMap(y = cells.all)
7. └─methods::new(...)
8. ├─methods::initialize(value, ...)
9. └─methods::initialize(value, ...)
10. └─methods (local) initMatrix(.Object, ...)
11. └─methods::validObject(.Object)
[ FAIL 3 | WARN 6 | SKIP 0 | PASS 154 ] Error: Test failures Execution halted ```

spqn

Version: 1.14.0
GitHub: https://github.com/hansenlab/spqn
Source code: https://github.com/cran/spqn
Date/Publication: 2023-10-24
Number of recursive dependencies: 77

Run revdep_details(, "spqn") for more info

checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘BiocGenerics’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

stabiliser

Version: 1.0.6
GitHub: NA
Source code: https://github.com/cran/stabiliser
Date/Publication: 2023-05-17 11:00:05 UTC
Number of recursive dependencies: 151

Run revdep_details(, "stabiliser") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘knitr’ All declared Imports should be used.

stapler

Version: 0.7.1
GitHub: https://github.com/muschellij2/stapler
Source code: https://github.com/cran/stapler
Date/Publication: 2020-01-09 18:50:06 UTC
Number of recursive dependencies: 67

Run revdep_details(, "stapler") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

stm

Version: 1.3.6.1
GitHub: https://github.com/bstewart/stm
Source code: https://github.com/cran/stm
Date/Publication: 2023-08-21 07:00:41 UTC
Number of recursive dependencies: 88

Run revdep_details(, "stm") for more info

checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: data 1.7Mb libs 3.2Mb
checking re-building of vignette outputs ... NOTE `` Error(s) in re-building vignettes: ... --- re-building ‘stmVignette.Rnw’ using Sweave stm v1.3.6.1 successfully loaded. See ?stm for help. Papers, resources, and other materials at structuraltopicmodel.com Error: processing vignette 'stmVignette.Rnw' failed with diagnostics: Running 'texi2dvi' on 'stmVignette.tex' failed. LaTeX errors: ! LaTeX Error: Fileulem.sty' not found.

... l.57 ^^M

! ==> Fatal error occurred, no output PDF file produced! --- failed re-building 'stmVignette.Rnw'

SUMMARY: processing the following file failed: 'stmVignette.Rnw'

Error: Vignette re-building failed. Execution halted ```

STROMA4

Version: 1.24.0
GitHub: NA
Source code: https://github.com/cran/STROMA4
Date/Publication: 2023-04-25
Number of recursive dependencies: 14

Run revdep_details(, "STROMA4") for more info

checking running R code from vignettes ... ``` ‘STROMA4-vignette.Rnw’... failed ERROR Errors in running code in vignettes: when running code in ‘STROMA4-vignette.Rnw’ ...

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") Installing package into ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/STROMA4/new/STROMA4.Rcheck’ (as ‘lib’ is unspecified)

When sourcing ‘STROMA4-vignette.R’: Error: trying to use CRAN without setting a mirror Execution halted ```
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘BiocManager’
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: ... --- re-building ‘STROMA4-vignette.Rnw’ using Sweave Installing package into ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/STROMA4/new/STROMA4.Rcheck’ (as ‘lib’ is unspecified)

Error: processing vignette 'STROMA4-vignette.Rnw' failed with diagnostics: chunk 1 Error in contrib.url(repos, type) : trying to use CRAN without setting a mirror

--- failed re-building ‘STROMA4-vignette.Rnw’

SUMMARY: processing the following file failed: ‘STROMA4-vignette.Rnw’

Error: Vignette re-building failed. Execution halted ```

summarytools

Version: 1.0.1
GitHub: https://github.com/dcomtois/summarytools
Source code: https://github.com/cran/summarytools
Date/Publication: 2022-05-20 07:30:05 UTC
Number of recursive dependencies: 85

Run revdep_details(, "summarytools") for more info

checking whether package ‘summarytools’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/summarytools/new/summarytools.Rcheck/00install.out’ for details.
checking data for non-ASCII characters ... NOTE Note: found 78 marked UTF-8 strings

susieR

Version: 0.12.35
GitHub: https://github.com/stephenslab/susieR
Source code: https://github.com/cran/susieR
Date/Publication: 2023-02-17 17:50:02 UTC
Number of recursive dependencies: 81

Run revdep_details(, "susieR") for more info

checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: --- re-building ‘finemapping.Rmd’ using rmarkdown --- finished re-building ‘finemapping.Rmd’

--- re-building ‘finemapping_summary_statistics.Rmd’ using rmarkdown --- finished re-building ‘finemapping_summary_statistics.Rmd’

--- re-building ‘mwe.Rmd’ using rmarkdown --- finished re-building ‘mwe.Rmd’

... l.8 \usepackage {xspace}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘trendfiltering_derivations.Rnw’

SUMMARY: processing the following file failed: ‘trendfiltering_derivations.Rnw’

Error: Vignette re-building failed. Execution halted ```

sva

Version: 3.50.0
GitHub: NA
Source code: https://github.com/cran/sva
Date/Publication: 2023-10-24
Number of recursive dependencies: 109

Run revdep_details(, "sva") for more info

checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘sva.Rnw’ using Sweave Loading required package: mgcv Loading required package: nlme This is mgcv 1.9-0. For overview type 'help("mgcv-package")'. Loading required package: genefilter Loading required package: BiocParallel Loading required package: Biobase Loading required package: BiocGenerics

... l.196 \RequirePackage {parnotes}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘sva.Rnw’

SUMMARY: processing the following file failed: ‘sva.Rnw’

Error: Vignette re-building failed. Execution halted ```

TCA

Version: 1.2.1
GitHub: https://github.com/cozygene/TCA
Source code: https://github.com/cran/TCA
Date/Publication: 2021-02-14 21:50:06 UTC
Number of recursive dependencies: 71

Run revdep_details(, "TCA") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Matrix’ ‘quadprog’ All declared Imports should be used.
checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

templateICAr

Version: 0.6.2
GitHub: https://github.com/mandymejia/templateICAr
Source code: https://github.com/cran/templateICAr
Date/Publication: 2023-01-27 09:10:02 UTC
Number of recursive dependencies: 110

Run revdep_details(, "templateICAr") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’
checking installed package size ... NOTE installed size is 13.3Mb sub-directories of 1Mb or more: libs 12.9Mb

tidybulk

Version: 1.13.1
GitHub: https://github.com/stemangiola/tidybulk
Source code: https://github.com/cran/tidybulk
Date/Publication: 2023-08-31
Number of recursive dependencies: 399

Run revdep_details(, "tidybulk") for more info

checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: ... --- re-building ‘introduction.Rmd’ using knitr

Quitting from lines 211-216 [plot_normalise] (introduction.Rmd) Error: processing vignette 'introduction.Rmd' failed with diagnostics: Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error in compute_aesthetics(): ! Aesthetics are not valid data columns. ... ✖ The following aesthetics are invalid: ✖ group = sample ℹ Did you mistype the name of a data column or forget to add after_stat()? --- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed: ‘introduction.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘pkgconfig’ Unexported objects imported by ':::' calls: ‘glmmSeq:::glmmTMBcore’ ‘glmmSeq:::hyp_matrix’ ‘glmmSeq:::lmer_wald’ ‘glmmSeq:::organiseStats’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .adjust_abundance_se: no visible binding for global variable ‘x’ .aggregate_duplicates_se: no visible binding for global variable ‘group_name’ .aggregate_duplicates_se: no visible binding for global variable ‘group’ .deconvolve_cellularity_se: no visible binding for global variable ‘X_cibersort’ .describe_transcript_SE: no visible binding for global variable ‘transcript’ .describe_transcript_SE: no visible binding for global variable ... parameter pathway predict prop rc read count ref_genome rotated dimensions sample 1 sample 2 sample a sample b sample_idx samples sdev seurat_clusters surv_test temp term test tot tot_filt transcript transcript_upper tt_columns update.formula upper value variable vcov web_page where x Consider adding importFrom("base", "sample") importFrom("stats", "AIC", "anova", "coef", "kmeans", "logLik", "predict", "update.formula", "vcov") to your NAMESPACE file.

topGO

Version: 2.54.0
GitHub: NA
Source code: https://github.com/cran/topGO
Date/Publication: 2023-10-24
Number of recursive dependencies: 59

Run revdep_details(, "topGO") for more info

checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi', 'SparseM' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking startup messages can be suppressed ... NOTE ```

groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘Rgraphviz’ ‘multtest’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing object imported by a ':::' call: ‘globaltest:::globaltest’
checking re-building of vignette outputs ... NOTE ``` Error(s) in re-building vignettes: --- re-building ‘topGO.Rnw’ using Sweave

Loading required package: xtable Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

... l.11 \usepackage {caption}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘topGO.Rnw’

SUMMARY: processing the following file failed: ‘topGO.Rnw’

Error: Vignette re-building failed. Execution halted ```

tradeSeq

Version: 1.16.0
GitHub: https://github.com/statOmics/tradeSeq
Source code: https://github.com/cran/tradeSeq
Date/Publication: 2023-10-24
Number of recursive dependencies: 181

Run revdep_details(, "tradeSeq") for more info

checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: doc 6.4Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Biobase’ ‘igraph’ All declared Imports should be used.
checking R code for possible problems ... NOTE .earlyDETest: no visible binding for global variable ‘X1’ .earlyDETest: no visible binding for global variable ‘X2’ .findKnots: no visible binding for global variable ‘t1’ .findKnots: no visible binding for global variable ‘l1’ .plotGeneCount: no visible binding for global variable ‘dim1’ .plotGeneCount: no visible binding for global variable ‘dim2’ .plotSmoothers: no visible binding for global variable ‘time’ .plotSmoothers: no visible binding for global variable ‘gene_count’ .plotSmoothers: no visible binding for global variable ‘lineage’ .plotSmoothers_conditions: no visible binding for global variable ... ‘pCol’ .plotSmoothers_sce: no visible binding for global variable ‘time’ .plotSmoothers_sce: no visible binding for global variable ‘gene_count’ .plotSmoothers_sce: no visible binding for global variable ‘lineage’ .plotSmoothers_sce: no visible binding for global variable ‘pCol’ Undefined global functions or variables: X1 X2 dim1 dim2 gene_count l1 lineage pCol t1 time Consider adding importFrom("stats", "time") to your NAMESPACE file.

TRESS

Version: 1.8.0
GitHub: NA
Source code: https://github.com/cran/TRESS
Date/Publication: 2023-10-24
Number of recursive dependencies: 107

Run revdep_details(, "TRESS") for more info

checking Rd files ... NOTE checkRd: (-1) CallCandidates.Rd:61: Escaped LaTeX specials: \& checkRd: (-1) CallCandidates.Rd:63: Escaped LaTeX specials: \& checkRd: (-1) CallPeaks.multiRep.Rd:7: Escaped LaTeX specials: \& checkRd: (-1) CallPeaks.paramEsti.Rd:10: Escaped LaTeX specials: \& checkRd: (-1) CallPeaks.paramEsti.Rd:23: Escaped LaTeX specials: \& checkRd: (-1) findBumps.Rd:8: Escaped LaTeX specials: \&

VanillaICE

Version: 1.64.0
GitHub: NA
Source code: https://github.com/cran/VanillaICE
Date/Publication: 2023-10-24
Number of recursive dependencies: 81

Run revdep_details(, "VanillaICE") for more info

checking Rd files ... WARNING checkRd: (5) VanillaICE.Rd:0-7: Must have a \description
checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'doMC', 'doMPI', 'doSNOW', 'doParallel', 'doRedis'
checking startup messages can be suppressed ... NOTE ``` No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’

It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. ```
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BSgenome.Hsapiens.UCSC.hg18’ ‘MatrixGenerics’ All declared Imports should be used.

VaSP

Version: 1.14.0
GitHub: https://github.com/yuhuihui2011/VaSP
Source code: https://github.com/cran/VaSP
Date/Publication: 2023-10-24
Number of recursive dependencies: 100

Run revdep_details(, "VaSP") for more info

checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: doc 3.6Mb extdata 3.4Mb

Voyager

Version: 1.4.0
GitHub: https://github.com/pachterlab/voyager
Source code: https://github.com/cran/Voyager
Date/Publication: 2023-10-26
Number of recursive dependencies: 228

Run revdep_details(, "Voyager") for more info

checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 50 lines of output: Error in `loadNamespace(x)`: there is no package called 'DropletUtils' Backtrace: ▆ 1. ├─SpatialFeatureExperiment::read10xVisiumSFE(".", images = "lowres") at test-plot.R:925:0 2. │ └─base::lapply(...) 3. │ └─SpatialFeatureExperiment (local) FUN(X[[i]], ...) ... • plot/plotcorrelogram-coldata-i.svg • plot/plotcorrelogram-continuous-color-by.svg • plot/plotcorrelogram-one-gene-c.svg • plot/plotcorrelogram-one-gene-corr.svg • plot/plotcorrelogram-specify-gene-and-coldata-i.svg • plot/plotdimloadings-not-balanced.svg • plot/with-subset-freqpoly.svg • plot/with-subset.svg Error: Test failures Execution halted
checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'variogram-internal.Rd': ‘variogram’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```
checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: doc 5.1Mb

vsclust

Version: 1.4.0
GitHub: NA
Source code: https://github.com/cran/vsclust
Date/Publication: 2023-10-24
Number of recursive dependencies: 182

Run revdep_details(, "vsclust") for more info

checking for code/documentation mismatches ... WARNING ``` Codoc mismatches from documentation object 'estimClustNum': estimClustNum Code: function(dat, maxClust = 25, scaling = "standardize", cores = 1) Docs: function(dat, maxClust = 25, cores = 1) Argument names in code not in docs: scaling Mismatches in argument names: Position: 3 Code: scaling Docs: cores

... runClustWrapper Code: function(dat, NClust, proteins = NULL, VSClust = TRUE, scaling = "standardize", cores, verbose = FALSE) Docs: function(dat, NClust, proteins = NULL, VSClust = TRUE, cores, verbose = FALSE) Argument names in code not in docs: scaling Mismatches in argument names: Position: 5 Code: scaling Docs: cores Position: 6 Code: cores Docs: verbose ```
checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: doc 4.4Mb libs 1.7Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE runFuncEnrich: no visible global function definition for ‘compareCluster’ runFuncEnrich: no visible global function definition for ‘new’ Undefined global functions or variables: compareCluster new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking Rd files ... NOTE prepare_Rd: vsclust-package.Rd:29-31: Dropping empty section \seealso prepare_Rd: vsclust-package.Rd:32-33: Dropping empty section \examples

wateRmelon

Version: 2.8.0
GitHub: NA
Source code: https://github.com/cran/wateRmelon
Date/Publication: 2023-10-24
Number of recursive dependencies: 194

Run revdep_details(, "wateRmelon") for more info

checking Rd metadata ... WARNING Rd files with duplicated alias 'fot': ‘dot-getManifestString.Rd’ ‘got.Rd’ Rd files with duplicated alias 'got': ‘dot-getManifestString.Rd’ ‘got.Rd’
checking for missing documentation entries ... WARNING Undocumented code objects: ‘epicv2clean’ ‘epicv2clean.default’ ‘epicv2clean.gds.class’ Undocumented data sets: ‘sex_coef’ Undocumented S4 methods: generic 'adjustedDasen' and siglist 'MethyLumiSet' generic 'adjustedDasen' and siglist 'MethylSet' generic 'adjustedDasen' and siglist 'RGChannelSet' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking Rd \usage sections ... WARNING ``` Undocumented arguments in documentation object '.getManifestString' ‘annotation’ Documented arguments not in \usage in documentation object '.getManifestString': ‘x’ ‘obj’ ‘fd’ ‘rn’

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'limma', 'matrixStats', 'methylumi', 'lumi', 'ROC', 'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'illuminaio' Adding so many packages to the search path is excessive and importing selectively is preferable.
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ ‘matrixStats’ ‘methylumi’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘minfi:::.annoGet’ ‘minfi:::.availableAnnotation’ ‘minfi:::.isRGOrStop’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .adjusted_normalizeFunnorm450k : unbiased_normalizeQuantiles: no visible global function definition for ‘colQuantiles’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘getMeth’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘getUnmeth’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘assay<-’ .buildControlMatrix450k: no visible global function definition for ‘colMeans2’ ... getMeth getNBeads getOOB getProbeInfo getProbeType getRed getSex getSnpBeta getUnmeth head hm27.controls hm27.ordering hm450.controls hm450.ordering intensitiesByChannel mapToGenome mclapply metadata methylated methylated<- methylumiR n.sd preprocessNoob preprocessRaw preprocessSWAN probeAnnotationsCategory projectName pval.detect<- pvals rowMeans2 seqnames sex_coef subsetByLoci unmethylated unmethylated<- warn Consider adding importFrom("utils", "head") to your NAMESPACE file.

WaverideR

Version: 0.3.2
GitHub: https://github.com/stratigraphy/WaverideR
Source code: https://github.com/cran/WaverideR
Date/Publication: 2023-09-06 15:40:02 UTC
Number of recursive dependencies: 160

Run revdep_details(, "WaverideR") for more info

checking whether package ‘WaverideR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/c4/home/henrik/repositories/matrixStats/revdep/checks/WaverideR/new/WaverideR.Rcheck/00install.out’ for details.

WeMix

Version: 4.0.0
GitHub: https://github.com/American-Institutes-for-Research/WeMix
Source code: https://github.com/cran/WeMix
Date/Publication: 2023-03-21 09:00:06 UTC
Number of recursive dependencies: 135

Run revdep_details(, "WeMix") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: --- re-building ‘Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/WeMix/new/WeMix.Rcheck/vign_test/WeMix/vignettes/Introduction_to_Mixed_Effects_Models_With_WeMix.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Introduction_to_Mixed_Effects_Models_With_WeMix.log for more info. --- failed re-building ‘Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd’ ... Error: processing vignette 'Weighted_Linear_Mixed_Effects_Models.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/WeMix/new/WeMix.Rcheck/vign_test/WeMix/vignettes/Weighted_Linear_Mixed_Effects_Models.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Weighted_Linear_Mixed_Effects_Models.log for more info. --- failed re-building ‘Weighted_Linear_Mixed_Effects_Models.Rmd’

SUMMARY: processing the following files failed: ‘Introduction_to_Mixed_Effects_Models_With_WeMix.Rmd’ ‘Weighted_Linear_Mixed_Effects_Models.Rmd’

Error: Vignette re-building failed. Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘EdSurvey’

WGCNA

Version: 1.72-1
GitHub: NA
Source code: https://github.com/cran/WGCNA
Date/Publication: 2023-01-18 12:10:05 UTC
Number of recursive dependencies: 110

Run revdep_details(, "WGCNA") for more info

checking Rd cross-references ... WARNING ``` Missing link or links in documentation object 'empiricalBayesLM.Rd': ‘rlm’

See section 'Cross-references' in the 'Writing R Extensions' manual. ```

yarn

Version: 1.28.0
GitHub: NA
Source code: https://github.com/cran/yarn
Date/Publication: 2023-10-24
Number of recursive dependencies: 179

Run revdep_details(, "yarn") for more info

checking re-building of vignette outputs ... WARNING `` Error(s) in re-building vignettes: ... --- re-building ‘yarn.Rmd’ using rmarkdown ! LaTeX Error: Fileiftex.sty' not found.

! Emergency stop.

Error: processing vignette 'yarn.Rmd' failed with diagnostics: LaTeX failed to compile /c4/home/henrik/repositories/matrixStats/revdep/checks/yarn/new/yarn.Rcheck/vign_test/yarn/vignettes/yarn.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See yarn.log for more info. --- failed re-building ‘yarn.Rmd’

SUMMARY: processing the following file failed: ‘yarn.Rmd’

Error: Vignette re-building failed. Execution halted ```

HenrikBengtsson/matrixStats documentation built on April 12, 2024, 5:32 a.m.

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Note that we can't provide technical support on individual packages. You should contact the package authors for that.

HenrikBengtsson/matrixStats Functions that Apply to Rows and Columns of Matrices (and to Vectors)

revdep/R_MATRIXSTATS_USENAMES_NA=defunct/problems.md In HenrikBengtsson/matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors)

abcrf

In both

AlpsNMR

In both

AMARETTO

In both

amplican

In both

aroma.core

In both

aroma.light

In both

autonomics

In both

Name: center

Title: Center samples

Aliases: center

** Examples

bahc

In both

BASiCS

In both

BatchQC

In both

BayesfMRI

In both

BayesianPlatformDesignTimeTrend

In both

baystability

In both

bigPint

In both

Name: plotClusters

Title: Plot static parallel coordinate clusters

Aliases: plotClusters

** Examples

The first set of five examples use data and dataMetrics

bingat

In both

BioNERO

In both

biscuiteer

In both

blackbox

In both

BloodGen3Module

In both

bnbc

In both

bnclassify

In both

bnem

In both

brms

In both

BSgenome

In both

Name: SNPlocs-class

Title: SNPlocs objects

Aliases: class:SNPlocs SNPlocs-class SNPlocs class:ODLT_SNPlocs

ODLT_SNPlocs-class ODLT_SNPlocs class:OldFashionSNPlocs

OldFashionSNPlocs-class OldFashionSNPlocs provider,SNPlocs-method

providerVersion,SNPlocs-method releaseDate,SNPlocs-method releaseName

releaseName,SNPlocs-method referenceGenome

BSW

In both

bulkAnalyseR

In both

bumphunter

In both

CARBayesST

In both

cardelino

In both

CATALYST

In both

causalOT

In both

HenrikBengtsson/matrixStats
Functions that Apply to Rows and Columns of Matrices (and to Vectors)

revdep/R_MATRIXSTATS_USENAMES_NA=defunct/problems.md
In HenrikBengtsson/matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors)